diff --git a/scripts/generate_pack.py b/scripts/generate_pack.py
index bf2cc84e..ca6124d4 100644
--- a/scripts/generate_pack.py
+++ b/scripts/generate_pack.py
@@ -1105,6 +1105,48 @@ def generate_pack(
             return None
         pack_systems = filtered
 
+    # Constrained-entry preference: platforms may declare the same
+    # destination several times (bare in one system, hash-constrained in
+    # another). First-come dedup would let the bare entry pack a wrong
+    # same-named file, so when a hash-constrained sibling resolves to a
+    # matching repo file, it claims the destination instead.
+    preferred_entries: dict[str, int] = {}
+    if source != "truth":
+        dest_entries: dict[str, list[dict]] = {}
+        for sys_id, system in sorted(pack_systems.items()):
+            for file_entry in system.get("files", []):
+                if required_only and file_entry.get("required") is False:
+                    continue
+                dest = _sanitize_path(
+                    file_entry.get("destination", file_entry.get("name", ""))
+                )
+                if not dest:
+                    continue
+                full = f"{base_dest}/{dest}" if base_dest else dest
+                dest_entries.setdefault(full, []).append(file_entry)
+        for full, entries in dest_entries.items():
+            if len(entries) < 2:
+                continue
+            constrained = [
+                fe
+                for fe in entries
+                if fe.get("md5") or fe.get("sha1") or fe.get("zipped_file")
+            ]
+            if not constrained:
+                continue
+            best = None
+            for fe in constrained:
+                _lp, _st = resolve_file(
+                    fe, db, bios_dir, zip_contents, data_dir_registry=data_registry
+                )
+                if _lp and _st == "md5_exact":
+                    best = fe
+                    break
+                if best is None and _lp and _st in ("exact", "zip_exact"):
+                    best = fe
+            if best is not None:
+                preferred_entries[full] = id(best)
+
     with zipfile.ZipFile(zip_path, "w", zipfile.ZIP_DEFLATED) as zf:
       if source != "truth":
         for sys_id, system in sorted(pack_systems.items()):
@@ -1131,6 +1173,10 @@ def generate_pack(
                     case_insensitive and dedup_key.lower() in seen_lower
                 )
 
+                preferred = preferred_entries.get(dedup_key)
+                if preferred is not None and id(file_entry) != preferred:
+                    continue
+
                 if _has_path_conflict(full_dest, seen_destinations, seen_parents):
                     continue
 
@@ -1348,7 +1394,7 @@ def generate_pack(
                 if extract and local_path.endswith(".zip"):
                     _extract_zip_to_archive(local_path, flat_dest, zf)
                 elif local_path.endswith(".zip"):
-                    _normalize_zip_for_pack(local_path, flat_dest, zf)
+                    _add_zip_to_pack(local_path, flat_dest, zf, file_entry)
                 else:
                     zf.write(local_path, flat_dest)
                 total_files += 1
@@ -1438,7 +1484,7 @@ def generate_pack(
 
           flat_dest = _flat(full_dest, base_dest, flatten)
           if local_path.endswith(".zip"):
-              _normalize_zip_for_pack(local_path, flat_dest, zf)
+              _add_zip_to_pack(local_path, flat_dest, zf, fe)
           else:
               zf.write(local_path, flat_dest)
           seen_destinations.add(full_dest)
@@ -1555,6 +1601,35 @@ def _extract_zip_to_archive(
             target_zf.writestr(target_path, data)
 
 
+def _add_zip_to_pack(
+    source_zip: str,
+    dest_path: str,
+    target_zf: zipfile.ZipFile,
+    file_entry: dict | None = None,
+):
+    """Write a source ZIP into the pack.
+
+    A declared outer hash (md5/sha1/crc32) means the platform or profile
+    verifies the ZIP bytes themselves (Batocera md5sum, System.dat), so
+    the resolved file is copied unchanged: a rebuild would change the
+    outer hash and fail the native check. Entries with zipped_file
+    declare the hash of a ROM inside the ZIP (checkInsideZip), which a
+    content-preserving rebuild does not affect.
+    """
+    if (
+        file_entry
+        and not file_entry.get("zipped_file")
+        and (
+            file_entry.get("md5")
+            or file_entry.get("sha1")
+            or file_entry.get("crc32")
+        )
+    ):
+        target_zf.write(source_zip, dest_path)
+        return
+    _normalize_zip_for_pack(source_zip, dest_path, target_zf)
+
+
 def _normalize_zip_for_pack(
     source_zip: str, dest_path: str, target_zf: zipfile.ZipFile
 ):
@@ -1755,7 +1830,7 @@ def generate_emulator_pack(
                 )
                 if local_path and status not in ("not_found",):
                     if local_path.endswith(".zip"):
-                        _normalize_zip_for_pack(local_path, archive_dest, zf)
+                        _add_zip_to_pack(local_path, archive_dest, zf, archive_entry)
                     else:
                         zf.write(local_path, archive_dest)
                     seen_destinations.add(archive_dest)
@@ -1837,7 +1912,7 @@ def generate_emulator_pack(
                     seen_hashes.add(dedup_key_hash)
 
                 if local_path.endswith(".zip"):
-                    _normalize_zip_for_pack(local_path, dest, zf)
+                    _add_zip_to_pack(local_path, dest, zf, fe)
                 else:
                     zf.write(local_path, dest)
                 seen_destinations.add(dest)
@@ -3118,8 +3193,14 @@ def generate_manifest(
         repo_path = _get_repo_path(sha1, db) if sha1 else ""
         source_emu = fe.get("source_emulator", "")
 
+        # Manifest dests are relative to base_destination; keep the inferred
+        # extras prefix when it is an internal layout dir (RetroDECK bios/).
+        manifest_dest = full_dest
+        if base_dest and manifest_dest.startswith(f"{base_dest}/"):
+            manifest_dest = manifest_dest[len(base_dest) + 1:]
+
         entry = {
-            "dest": dest,
+            "dest": manifest_dest,
             "sha1": sha1,
             "size": file_size,
             "repo_path": repo_path,
@@ -3413,6 +3494,133 @@ def generate_sha256sums(output_dir: str) -> str | None:
     return sums_path
 
 
+def _hash_matches(declared: str, actual: str) -> bool:
+    """Compare a declared hash value against an actual hex digest.
+
+    Handles comma-separated multi-hash lists and uppercase (Recalbox)
+    and truncated MD5s (Batocera 29-char): a declared value shorter
+    than the digest matches by prefix.
+    """
+    actual = actual.lower()
+    for cand in declared.split(","):
+        cand = cand.strip().lower()
+        if not cand:
+            continue
+        if len(cand) < len(actual):
+            if actual.startswith(cand):
+                return True
+        elif actual == cand:
+            return True
+    return False
+
+
+def _check_member_hash(
+    zf: zipfile.ZipFile, member: str, file_entry: dict, mode: str
+) -> str | None:
+    """Verify a pack member against its platform-declared hash.
+
+    Reproduces the platform's native check inside the pack: md5/sha1 of
+    the member bytes, or checkInsideZip when zipped_file is set
+    (Batocera hashes a ROM inside the ZIP, matched case-insensitively).
+    Returns an error string, or None when the member passes.
+    """
+    declared = str(file_entry.get(mode) or "").strip()
+    if not declared:
+        return None
+
+    zipped_file = file_entry.get("zipped_file")
+    if zipped_file:
+        import io
+
+        try:
+            with zipfile.ZipFile(io.BytesIO(zf.read(member))) as inner:
+                want = zipped_file.casefold()
+                target = next(
+                    (n for n in inner.namelist() if n.casefold() == want), None
+                )
+                if target is None:
+                    return f"{member}: {zipped_file} not found inside ZIP"
+                actual = hashlib.md5(inner.read(target)).hexdigest()
+        except zipfile.BadZipFile:
+            return f"{member}: not a valid ZIP"
+        if not _hash_matches(declared, actual):
+            return (
+                f"{member}: {zipped_file} inside-zip md5 {actual} "
+                f"!= declared {declared}"
+            )
+        return None
+
+    h = hashlib.md5() if mode == "md5" else hashlib.sha1()
+    with zf.open(member) as f:
+        for chunk in iter(lambda: f.read(65536), b""):
+            h.update(chunk)
+    actual = h.hexdigest()
+    if _hash_matches(declared, actual):
+        return None
+
+    # Recalbox Md5Composite: MD5 over sorted inner contents of a ZIP,
+    # independent of compression and metadata (Zip::Md5Composite()).
+    if mode == "md5" and member.endswith(".zip"):
+        import io
+
+        try:
+            with zipfile.ZipFile(io.BytesIO(zf.read(member))) as inner:
+                names = sorted(n for n in inner.namelist() if not n.endswith("/"))
+                ch = hashlib.md5()
+                for n in names:
+                    ch.update(inner.read(n))
+            if _hash_matches(declared, ch.hexdigest()):
+                return None
+        except (zipfile.BadZipFile, OSError):
+            pass
+
+    return f"{member}: {mode} {actual} != declared {declared}"
+
+
+def _repo_satisfies_declaration(
+    entries: list[dict], db: dict, mode: str
+) -> bool:
+    """Check whether any repo file matches one of the declared hashes.
+
+    Used to separate pack divergence (a matching file exists but was not
+    packed) from data coverage gaps (no repo file matches the upstream
+    declaration): only the former is a pack generation error.
+    """
+    from common import md5_composite
+
+    files_db = db.get("files", {})
+    by_md5 = db.get("indexes", {}).get("by_md5", {})
+    by_name = db.get("indexes", {}).get("by_name", {})
+
+    for fe in entries:
+        declared = str(fe.get(mode) or "").strip()
+        if not declared:
+            continue
+        hashes = [h.strip().lower() for h in declared.split(",") if h.strip()]
+        for h in hashes:
+            if mode == "sha1":
+                entry = files_db.get(h)
+            else:
+                entry = files_db.get(by_md5.get(h, ""))
+            if entry and os.path.exists(entry.get("path", "")):
+                return True
+        if mode == "md5":
+            hash_set = set(hashes)
+            for cand_sha in by_name.get(fe.get("name", ""), []):
+                entry = files_db.get(cand_sha)
+                if not entry:
+                    continue
+                path = entry.get("path", "")
+                if not path.endswith(".zip") or not os.path.exists(path):
+                    continue
+                try:
+                    if md5_composite(path).lower() in hash_set:
+                        return True
+                except (zipfile.BadZipFile, OSError):
+                    continue
+    return False
+
+
 def verify_pack_against_platform(
     zip_path: str,
     platform_name: str,
@@ -3478,9 +3686,11 @@ def verify_pack_against_platform(
                 ):
                     errors.append(f"zero-byte: {info.filename}")
 
-        # 1. Baseline file presence
+        # 1. Baseline file presence + native hash check
+        verification_mode = config.get("verification_mode", "existence")
         baseline_checked = 0
         baseline_present = 0
+        decl_by_member: dict[str, list[dict]] = {}
         for sys_id, system in config.get("systems", {}).items():
             for fe in system.get("files", []):
                 dest = fe.get("destination", fe.get("name", ""))
@@ -3489,10 +3699,45 @@ def verify_pack_against_platform(
                 expected = f"{base_dest}/{dest}" if base_dest and not is_flat else dest
                 baseline_checked += 1
 
-                if expected in zip_set or expected.lower() in zip_lower:
-                    baseline_present += 1
+                if expected in zip_set:
+                    member = expected
+                elif expected.lower() in zip_lower:
+                    member = zip_lower[expected.lower()]
                 else:
                     errors.append(f"baseline missing: {expected}")
+                    continue
+                baseline_present += 1
+                decl_by_member.setdefault(member, []).append(fe)
+
+        # Reproduce the platform's native hash check on pack bytes.
+        # A destination declared by several entries passes when the packed
+        # member satisfies any of them. A failure only counts as a pack
+        # error when the repo holds a file matching a declaration: without
+        # one, the pack ships its best effort and the gap is a data issue
+        # reported by verify.py, not a generation bug.
+        if verification_mode in ("md5", "sha1"):
+            for member, decl_entries in decl_by_member.items():
+                checkable = [
+                    fe
+                    for fe in decl_entries
+                    if str(fe.get(verification_mode) or "").strip()
+                ]
+                if not checkable:
+                    continue
+                member_errors = []
+                satisfied = False
+                for fe in checkable:
+                    err = _check_member_hash(zf, member, fe, verification_mode)
+                    if err is None:
+                        satisfied = True
+                        break
+                    member_errors.append(err)
+                if satisfied:
+                    continue
+                if db is None or _repo_satisfies_declaration(
+                    checkable, db, verification_mode
+                ):
+                    errors.append(member_errors[0])
 
         # 2. Core extras presence (files from emulator profiles, in repo)
         #    Mirror the pack builder's skip logic: only count files that
diff --git a/tests/test_e2e.py b/tests/test_e2e.py
index b3435c91..1cd33854 100644
--- a/tests/test_e2e.py
+++ b/tests/test_e2e.py
@@ -4702,6 +4702,184 @@ struct BurnDriver BurnDrvneogeo = {
         self.assertEqual(len(zips), 6, f"Expected 6 ZIPs, got {len(zips)}: {zips}")
         self.assertEqual(len(set(zips)), 6)
 
+    def _make_hash_zip_fixture(self, tmpdir, declare_md5=True):
+        """Platform fixture with one ZIP file, optionally md5-declared."""
+        import hashlib as hl
+
+        plat_dir = os.path.join(tmpdir, "platforms")
+        bios_dir = os.path.join(tmpdir, "bios", "Arcade")
+        out_dir = os.path.join(tmpdir, "dist")
+        os.makedirs(plat_dir)
+        os.makedirs(bios_dir)
+
+        zip_src = os.path.join(bios_dir, "testbios.zip")
+        with zipfile.ZipFile(zip_src, "w", zipfile.ZIP_DEFLATED) as zf:
+            info = zipfile.ZipInfo("rom.bin", date_time=(2020, 6, 15, 12, 0, 0))
+            zf.writestr(info, b"rom_content_bytes")
+        from common import compute_hashes
+
+        h = compute_hashes(zip_src)
+
+        db = {
+            "files": {
+                h["sha1"]: {
+                    "name": "testbios.zip",
+                    "md5": h["md5"],
+                    "sha1": h["sha1"],
+                    "path": zip_src,
+                    "paths": ["Arcade/testbios.zip"],
+                },
+            },
+            "indexes": {
+                "by_md5": {h["md5"]: h["sha1"]},
+                "by_name": {"testbios.zip": [h["sha1"]]},
+                "by_crc32": {},
+                "by_path_suffix": {},
+            },
+        }
+        entry = {"name": "testbios.zip", "destination": "dc/testbios.zip"}
+        if declare_md5:
+            entry["md5"] = h["md5"]
+        config = {
+            "platform": "HashZipTest",
+            "verification_mode": "md5",
+            "base_destination": "bios",
+            "systems": {"arcade-sys": {"files": [entry]}},
+        }
+        with open(os.path.join(plat_dir, "test_hashzip.yml"), "w") as fh:
+            yaml.dump(config, fh)
+        return plat_dir, os.path.join(tmpdir, "bios"), out_dir, db, h, hl
+
+    def test_210_pack_copies_md5_declared_zip_byte_identical(self):
+        """md5-declared ZIPs are copied unchanged, never rebuilt."""
+        import tempfile
+
+        from generate_pack import generate_pack
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            plat_dir, bios_root, out_dir, db, h, hl = self._make_hash_zip_fixture(
+                tmpdir, declare_md5=True
+            )
+            zip_path = generate_pack(
+                "test_hashzip", plat_dir, db, bios_root, out_dir
+            )
+            self.assertIsNotNone(zip_path)
+            with zipfile.ZipFile(zip_path) as zf:
+                data = zf.read("dc/testbios.zip")
+            self.assertEqual(hl.md5(data).hexdigest(), h["md5"])
+
+    def test_211_pack_rebuilds_zip_without_declared_hash(self):
+        """ZIPs without declared hash are rebuilt deterministically."""
+        import io
+        import tempfile
+
+        from generate_pack import generate_pack
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            plat_dir, bios_root, out_dir, db, h, hl = self._make_hash_zip_fixture(
+                tmpdir, declare_md5=False
+            )
+            zip_path = generate_pack(
+                "test_hashzip", plat_dir, db, bios_root, out_dir
+            )
+            self.assertIsNotNone(zip_path)
+            with zipfile.ZipFile(zip_path) as zf:
+                data = zf.read("dc/testbios.zip")
+            # Outer hash differs (1980 timestamps), inner content identical
+            self.assertNotEqual(hl.md5(data).hexdigest(), h["md5"])
+            with zipfile.ZipFile(io.BytesIO(data)) as inner:
+                self.assertEqual(inner.read("rom.bin"), b"rom_content_bytes")
+
+    def test_212_verify_pack_flags_native_md5_mismatch(self):
+        """Pack verification reproduces the native md5 check per member."""
+        import tempfile
+
+        from generate_pack import verify_pack_against_platform
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            plat_dir, bios_root, out_dir, db, h, hl = self._make_hash_zip_fixture(
+                tmpdir, declare_md5=True
+            )
+            os.makedirs(out_dir)
+            bad_pack = os.path.join(out_dir, "HashZipTest_BIOS_Pack.zip")
+            with zipfile.ZipFile(bad_pack, "w") as zf:
+                zf.writestr("dc/testbios.zip", b"wrong bytes entirely")
+            result = verify_pack_against_platform(
+                bad_pack, "test_hashzip", plat_dir, db=None
+            )
+            errors = result[3]
+            self.assertTrue(
+                any("md5" in e for e in errors),
+                f"expected md5 mismatch error, got: {errors}",
+            )
+
+    def test_213_verify_pack_passes_correct_member_hash(self):
+        """Pack verification passes when member bytes match declared md5."""
+        import tempfile
+
+        from generate_pack import verify_pack_against_platform
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            plat_dir, bios_root, out_dir, db, h, hl = self._make_hash_zip_fixture(
+                tmpdir, declare_md5=True
+            )
+            os.makedirs(out_dir)
+            good_pack = os.path.join(out_dir, "HashZipTest_BIOS_Pack.zip")
+            src = os.path.join(bios_root, "Arcade", "testbios.zip")
+            with zipfile.ZipFile(good_pack, "w") as zf:
+                zf.write(src, "dc/testbios.zip")
+            result = verify_pack_against_platform(
+                good_pack, "test_hashzip", plat_dir, db=None
+            )
+            self.assertEqual(result[3], [], f"unexpected errors: {result[3]}")
+
+    def test_214_hash_matches_truncated_and_multi(self):
+        """Declared-hash compare handles truncation, case, multi-values."""
+        from generate_pack import _hash_matches
+
+        full = "85254fbe320ca82a768ec2c26bb08def"
+        self.assertTrue(_hash_matches(full, full))
+        self.assertTrue(_hash_matches(full.upper(), full))
+        self.assertTrue(_hash_matches(full[:29], full))  # Batocera truncated
+        self.assertTrue(_hash_matches(f"deadbeef, {full}", full))
+        self.assertFalse(_hash_matches("0" * 32, full))
+        self.assertFalse(_hash_matches("", full))
+
+    def test_215_check_member_hash_inside_zip(self):
+        """zipped_file entries verify the ROM inside the ZIP, not the ZIP."""
+        import hashlib as hl
+        import tempfile
+
+        from generate_pack import _check_member_hash
+
+        rom = b"inner rom bytes"
+        rom_md5 = hl.md5(rom).hexdigest()
+        with tempfile.TemporaryDirectory() as tmpdir:
+            pack = os.path.join(tmpdir, "pack.zip")
+            import io
+
+            inner_buf = io.BytesIO()
+            with zipfile.ZipFile(inner_buf, "w") as inner:
+                inner.writestr("EPR-123.IC27", rom)
+            with zipfile.ZipFile(pack, "w") as zf:
+                zf.writestr("dc/game.zip", inner_buf.getvalue())
+            with zipfile.ZipFile(pack) as zf:
+                # Case-insensitive inner match (Batocera casefold)
+                ok = _check_member_hash(
+                    zf,
+                    "dc/game.zip",
+                    {"zipped_file": "epr-123.ic27", "md5": rom_md5},
+                    "md5",
+                )
+                self.assertIsNone(ok)
+                bad = _check_member_hash(
+                    zf,
+                    "dc/game.zip",
+                    {"zipped_file": "epr-123.ic27", "md5": "0" * 32},
+                    "md5",
+                )
+                self.assertIsNotNone(bad)
+
 
 if __name__ == "__main__":
     unittest.main()