diff --git a/docs/research/coordination.md b/docs/research/coordination.md
index e700933860..183412d5bc 100644
--- a/docs/research/coordination.md
+++ b/docs/research/coordination.md
@@ -88,6 +88,11 @@ Joined path results show `head`/`base` for the file snapshot,
 `body_head`/`body_base` for PR metadata, and separate `head_matches` and
 `base_matches` flags. Check both flags and `truncated`. Coverage also lists
 `unverified_heads` and `unverified_bases`, even when no path matches the query.
+It also lists PRs with unavailable file lists or advertised-count shortfalls
+in `truncated_prs`, with a warning even when those PRs do not match
+the requested path or fall outside `--limit`. A true `complete_pagination`
+means the list paging finished; it does not mean every PR's file inventory
+is complete. Term-and-path intersections retain each match's `truncated` flag.
 A missing legacy base remains unknown; it is never copied from another snapshot.
 Online path queries refresh endpoint-incomplete sources. Offline or failed
 refreshes keep the old evidence and explicitly report the missing binding.
diff --git a/scripts/find_overlap.py b/scripts/find_overlap.py
index 3e64e98477..bfc534e8b3 100644
--- a/scripts/find_overlap.py
+++ b/scripts/find_overlap.py
@@ -421,6 +421,11 @@ def main():
         coverage["pr_files"] = {k: source[k] for k in ("fetched_at", "complete_pagination")} if source else None
         if source:
             coverage["pr_files"]["records"] = len(source["records"])
+            truncated = sorted({row["number"] for row in source["records"] if row.get("truncated", False)})
+            coverage["pr_files"]["truncated_prs"] = truncated
+            if truncated:
+                warnings.append(f"pr_files: incomplete file inventories for {len(truncated)} PRs; "
+                                "paths may be missing. Check truncated_prs in coverage, even when no path matches.")
             pulls = snapshot["sources"].get("open_prs", {"records": []})["records"]
             heads = {pull["number"]: pull.get("head") for pull in pulls}
             file_heads = {row["number"]: row.get("head") for row in source["records"]}
@@ -445,7 +450,7 @@ def main():
         hits = {m["number"]: m for m in path_matches}
         matches = [dict(m, **{key: hits[m["number"]][key]
                              for key in ("matched_paths", "head", "body_head", "head_matches",
-                                         "base", "body_base", "base_matches")}) for m in matches
+                                         "base", "body_base", "base_matches", "truncated")}) for m in matches
                    if m.get("kind") == "pr" and m.get("number") in hits]
     if patterns and not any(t.strip() for t in terms):
         matches = []
@@ -462,7 +467,9 @@ def main():
         report["path_patterns"] = patterns
         report["path_limits"] = ("Path matching covers the changed file paths GitHub reports for open PRs, "
                                  "not diff contents; all available file pages are followed. Missing lists or "
-                                 "advertised-count shortfalls are flagged truncated. Head/base identify the file "
+                                 "advertised-count shortfalls are flagged truncated and listed in coverage.pr_files.truncated_prs "
+                                 "independently of matches or --limit. complete_pagination describes list paging, "
+                                 "not completeness of each PR's file inventory. Head/base identify the file "
                                  "snapshot; body_head/body_base identify PR metadata. Both endpoints must match. "
                                  "This is not an atomic server snapshot. Unverified joins are flagged, "
                                  "including inventories with no matching path.")
@@ -485,7 +492,8 @@ def main():
             print("WARNING: " + warning)
         print(f"{len(matches)} possible matches; showing {min(args.limit, len(matches))}")
         for match in matches[:args.limit]:
-            print(f"\n[{match['kind']}] {match['title']}\n{match.get('url', match.get('path'))}")
+            flags = " (file list truncated)" if match.get("truncated") else ""
+            print(f"\n[{match['kind']}] {match['title']}{flags}\n{match.get('url', match.get('path'))}")
             if match.get("head"):
                 print("Head: " + match["head"])
             if match.get("head_matches") is False:
diff --git a/tests/test_research_pr_inventory_coverage.py b/tests/test_research_pr_inventory_coverage.py
new file mode 100644
index 0000000000..16e4a40cba
--- /dev/null
+++ b/tests/test_research_pr_inventory_coverage.py
@@ -0,0 +1,92 @@
+"""Known file-inventory gaps must survive filtering and result limits."""
+from datetime import datetime, timezone
+import json
+import os
+from pathlib import Path
+import subprocess
+import sys
+import tempfile
+import unittest
+
+
+ROOT = Path(__file__).resolve().parents[1]
+SCRIPT = ROOT / 'scripts/find_overlap.py'
+
+
+class InventoryCoverageTests(unittest.TestCase):
+    def run_cli(self, inventories, *arguments):
+        with tempfile.TemporaryDirectory() as directory:
+            cache = Path(directory) / 'overlap.json'
+            bodies = [dict(kind='pr', number=row['number'], title='needle', body='',
+                           head=row['head'], base=row['base'], state='open',
+                           url=f"https://example.invalid/{row['number']}",
+                           updated_at='2026-10-18T00:00:00Z') for row in inventories]
+            fetched_at = datetime.now(timezone.utc).isoformat()
+            sources = {name: dict(fetched_at=fetched_at, complete_pagination=True, records=rows)
+                       for name, rows in [('open_prs', bodies), ('discussions', []),
+                                          ('pr_files', inventories)]}
+            original = json.dumps(dict(schema_version=1, repository='CrocSwap/integer-mult-bounds',
+                                       sources=sources)).encode('utf-8')
+            cache.write_bytes(original)
+            # A fresh synthetic snapshot must not require gh or any network call.
+            result = subprocess.run([sys.executable, '-B', str(SCRIPT), '--cache', str(cache),
+                                     '--max-age', '3600', *arguments], capture_output=True,
+                                    encoding='utf-8', timeout=30, env={**os.environ, 'PATH': ''})
+            self.assertEqual(result.returncode, 0, result.stderr)
+            self.assertEqual(cache.read_bytes(), original)
+            return result.stdout
+
+    @staticmethod
+    def row(number, paths, truncated):
+        return dict(number=number, head='a' * 40, base='b' * 40,
+                    paths=paths, truncated=truncated)
+
+    def test_unavailable_and_short_inventories_warn_even_without_a_hit(self):
+        rows = [self.row(376, [], True), self.row(377, ['elsewhere.py'], True)]
+        for options in ([], ['--offline']):
+            with self.subTest(options=options):
+                report = json.loads(self.run_cli(rows, '--path', 'missing.py', '--json', *options))
+                coverage = report['coverage']['pr_files']
+                self.assertTrue(coverage['complete_pagination'])
+                self.assertEqual(coverage['truncated_prs'], [376, 377])
+                self.assertEqual(coverage['unverified_heads'], [])
+                self.assertEqual(coverage['unverified_bases'], [])
+                self.assertEqual(report['path_matches_total'], 0)
+                self.assertTrue(any('incomplete file inventories for 2 PRs' in warning
+                                    for warning in report['warnings']))
+
+    def test_result_limit_does_not_hide_incomplete_inventories(self):
+        rows = [self.row(98, ['elsewhere.py'], True), self.row(99, [], True),
+                self.row(100, ['target.py'], True), self.row(101, ['target.py'], False),
+                self.row(99, [], True)]
+        report = json.loads(self.run_cli(rows, '--path', 'target.py', '--limit', '1', '--json'))
+        self.assertEqual(report['path_matches_total'], 2)
+        self.assertEqual([row['number'] for row in report['path_matches']], [101])
+        self.assertFalse(report['path_matches'][0]['truncated'])
+        self.assertEqual(report['coverage']['pr_files']['truncated_prs'], [98, 99, 100])
+        self.assertTrue(any('incomplete file inventories for 3 PRs' in warning
+                            for warning in report['warnings']))
+
+    def test_combined_term_and_path_matches_preserve_truncation(self):
+        rows = [self.row(100, ['target.py'], True), self.row(101, ['target.py'], False)]
+        report = json.loads(self.run_cli(rows, 'needle', '--path', 'target.py', '--json'))
+        self.assertEqual({row['number']: row['truncated'] for row in report['matches']},
+                         {100: True, 101: False})
+
+    def test_text_report_surfaces_unmatched_gaps_and_combined_match_flags(self):
+        rows = [self.row(376, [], True)]
+        output = self.run_cli(rows, '--path', 'missing.py')
+        self.assertIn('"truncated_prs": [376]', output)
+        self.assertIn('WARNING: pr_files: incomplete file inventories for 1 PRs', output)
+        output = self.run_cli([self.row(100, ['target.py'], True)], 'needle', '--path', 'target.py')
+        self.assertIn('[pr] needle (file list truncated)', output)
+
+    def test_complete_empty_inventory_is_not_reported_as_a_gap(self):
+        report = json.loads(self.run_cli([self.row(376, [], False)], '--path', 'missing.py', '--json'))
+        self.assertEqual(report['coverage']['pr_files']['truncated_prs'], [])
+        self.assertEqual(report['warnings'], [])
+        self.assertEqual(report['path_matches_total'], 0)
+
+
+if __name__ == '__main__':
+    unittest.main()