diff --git a/scripts/export_native.py b/scripts/export_native.py
index 324f4faf..5920694a 100644
--- a/scripts/export_native.py
+++ b/scripts/export_native.py
@@ -122,6 +122,24 @@ def fetch(
     return payload
 
 
+def _remove_stale(platform_dir: Path, produced: set[str]) -> None:
+    """Remove what an earlier run wrote and this one does not.
+
+    RetroPie writes one scriptmodule per package it corrects and RetroDECK one
+    manifest per component: a package corrected by an older truth kept its
+    file beside a report saying it was no longer touched, and the directory
+    contradicted the run.
+    """
+    if not platform_dir.is_dir():
+        return
+    for path in sorted(platform_dir.rglob("*"), reverse=True):
+        relative = path.relative_to(platform_dir).as_posix()
+        if path.is_file() and relative not in produced:
+            path.unlink()
+        elif path.is_dir() and not any(path.iterdir()):
+            path.rmdir()
+
+
 def pinned_base(wanted: dict[str, str], scraped: dict | None) -> str:
     """The revision our transcription came from, when the YAML records it.
 
@@ -362,6 +380,7 @@ def export_platform(
     issues = exporter.validate(systems, produced)
 
     platform_dir = output_dir / platform
+    _remove_stale(platform_dir, set(produced))
     for relative, content in produced.items():
         path = platform_dir / relative
         path.parent.mkdir(parents=True, exist_ok=True)
diff --git a/tests/test_exporters.py b/tests/test_exporters.py
index 1039758d..f8064b4c 100644
--- a/tests/test_exporters.py
+++ b/tests/test_exporters.py
@@ -784,6 +784,34 @@ class RommExport(unittest.TestCase):
         self.assertTrue(all(k.startswith("psx:") for k in data))
 
 
+class AnExportLeavesNoStaleFile(unittest.TestCase):
+    """RetroPie writes one scriptmodule per corrected package. A second run on
+    a fresher truth printed "2 packages corrected" over a directory still
+    holding the six files of the first run."""
+
+    def test_files_this_run_does_not_write_are_removed(self):
+        import export_native  # noqa: PLC0415
+
+        with tempfile.TemporaryDirectory() as tmp:
+            root = Path(tmp) / "retropie"
+            (root / "scriptmodules" / "libretrocores").mkdir(parents=True)
+            kept = root / "scriptmodules" / "libretrocores" / "lr-mgba.sh"
+            stale = root / "scriptmodules" / "libretrocores" / "lr-pcsx-rearmed.sh"
+            gone_dir = root / "scriptmodules" / "emulators"
+            gone_dir.mkdir()
+            for path in (kept, stale, gone_dir / "pcsx-rearmed.sh"):
+                path.write_text("old", encoding="utf-8")
+            export_native._remove_stale(root, {"scriptmodules/libretrocores/lr-mgba.sh"})
+            self.assertTrue(kept.exists())
+            self.assertFalse(stale.exists())
+            self.assertFalse(gone_dir.exists())
+
+    def test_the_export_clears_before_it_writes(self):
+        source = (REPO_ROOT / "scripts" / "export_native.py").read_text()
+        body = source[source.index("def export_platform("):]
+        self.assertLess(body.index("_remove_stale("), body.index(".write_text("))
+
+
 class RommKeepsItsFixture(unittest.TestCase):
     """The export rebuilt known_bios_files.json from our model in our order:
     3 hash corrections came out as a 3116-line diff, and a key RomM had that