diff --git a/emulators/nestopia.yml b/emulators/nestopia.yml
index 317c2528..89dd0ae0 100644
--- a/emulators/nestopia.yml
+++ b/emulators/nestopia.yml
@@ -5,7 +5,7 @@ source: "https://github.com/libretro/nestopia"
 upstream: "https://gitlab.com/jgemu/nestopia"
 logo: "https://raw.githubusercontent.com/0ldsk00l/nestopia/master/icons/svg/nestopia.svg"
 profiled_date: "2026-03-24"
-source_commit: "d0f461cee801c509748606e91c8ff0563ef62cd6"
+source_commit: "5a1cd378cb46ca9ccc2dd6f8b2b6a79ab986052e"
 core_version: "1.53.1"
 display_name: "Nintendo - NES / Famicom (Nestopia)"
 cores: [nestopia]
diff --git a/scripts/profile_sync.py b/scripts/profile_sync.py
index 76949537..2b029f00 100644
--- a/scripts/profile_sync.py
+++ b/scripts/profile_sync.py
@@ -740,6 +740,15 @@ def locate_by_declared_value(
     return None
 
 
+def _written_against_head(part, head_lines) -> bool:
+    """Whether the cited line exists at HEAD, which is where it was written."""
+    return (
+        head_lines is not None
+        and part.start is not None
+        and part.start <= len(head_lines)
+    )
+
+
 def anchor_part(
     part: RefPart, fetch, rename_getter, describe=None, tokens=()
 ) -> PartResult:
@@ -820,10 +829,20 @@ def anchor_part(
         # still names an older revision. Saying "missing" sends the reader
         # hunting for a move that never happened; the fix is the pin.
         reason = "pin revision missing"
-        if head_lines is not None and part.start <= len(head_lines):
+        if _written_against_head(part, head_lines):
             reason = "written against HEAD, pin names an older revision"
         return PartResult(part, "GONE", None, None, None, [], reason, slug, url)
 
+    if part.start > len(pin_lines) and _written_against_head(part, head_lines):
+        # The file is there and the line is not yet: the pinned revision is
+        # shorter than the one the ref was written against. nestopia cited
+        # the palette and database loads at 2041 and 2063, which is where
+        # HEAD carries them, over a pin four hundred lines shorter.
+        return PartResult(
+            part, "GONE", None, None, None, [],
+            "written against HEAD, pin names an older revision", slug, url,
+        )
+
     end = part.end or part.start
     anchored = anchor_block(pin_lines, head_lines, part.start, end)
     note = anchored.reason
diff --git a/tests/test_profile_sync.py b/tests/test_profile_sync.py
index 364697c7..659af9e3 100644
--- a/tests/test_profile_sync.py
+++ b/tests/test_profile_sync.py
@@ -1499,6 +1499,21 @@ class TestRefsAheadOfTheirPin(TestBuildReport):
             part.reason, "written against HEAD, pin names an older revision"
         )
 
+    def test_a_range_past_the_pin_file_but_inside_head_names_the_pin(self):
+        """nestopia's shape: the file is there, the line is not yet.
+
+        Palette and database loads sat at 2041 and 2063, which is where HEAD
+        carries them; the pinned revision was four hundred lines shorter.
+        """
+        self.files[("pinsha", "a.c")] = ["x"] * 10
+        self.files[("headsha", "a.c")] = ["x"] * 40 + ["the cited line"] + ["y"]
+        report = build_report("test", self._profile(["a.c:41"]), self.dir)
+        part = report.entries[0].parts[0]
+        self.assertEqual(part.status, "GONE")
+        self.assertEqual(
+            part.reason, "written against HEAD, pin names an older revision"
+        )
+
     def test_a_range_beyond_head_is_still_just_missing(self):
         """Not every pin miss is a stale pin; only one that fits HEAD."""
         self.files[("headsha", "a.c")] = ["x"]