diff --git a/lib/python/base_cli/_runtime.py b/lib/python/base_cli/_runtime.py
index 8f82414..e358126 100644
--- a/lib/python/base_cli/_runtime.py
+++ b/lib/python/base_cli/_runtime.py
@@ -75,8 +75,11 @@ def prune_log_files(
     tracked = _read_log_index(index_path)
     if tracked is None:
         tracked = {path.resolve() for path in log_dir.glob("*/logs/*.log")}
-    tracked.add(current_log_file.resolve())
-    candidates = [(path.name, path) for path in tracked if not _same_path(path, current_log_file)]
+    current_log_file = current_log_file.resolve()
+    tracked = {path.resolve() for path in tracked}
+    tracked = {path for path in tracked if path.exists() or path == current_log_file}
+    tracked.add(current_log_file)
+    candidates = [(path.name, path) for path in tracked if path != current_log_file]
 
     excess_count = len(candidates) + 1 - max_log_files
     if excess_count > 0:
@@ -87,7 +90,7 @@ def prune_log_files(
             except OSError as exc:
                 logger.warning("Could not prune log file '%s': %s", path, exc)
 
-    tracked = {path for path in tracked if path.exists() or _same_path(path, current_log_file)}
+    tracked = {path for path in tracked if path.exists() or path == current_log_file}
     try:
         write_private_json(index_path, {"version": 1, "logs": sorted(str(path) for path in tracked)})
     except (OSError, TypeError, ValueError) as exc:
@@ -121,10 +124,3 @@ def _runtime_directory_error(path: Path, cache_root: Path, exc: OSError) -> str:
         f"Check permissions on that directory. If the Base cache root '{cache_root}' is unusable, "
         "set BASE_CACHE_DIR to a writable directory."
     )
-
-
-def _same_path(left: Path, right: Path) -> bool:
-    try:
-        return left.resolve() == right.resolve()
-    except OSError:
-        return left.absolute() == right.absolute()
diff --git a/tests/test_app_log_retention.py b/tests/test_app_log_retention.py
index 9d24228..aee4ac4 100644
--- a/tests/test_app_log_retention.py
+++ b/tests/test_app_log_retention.py
@@ -1,6 +1,8 @@
 from __future__ import annotations
 
 import importlib.util
+import json
+import logging
 import os
 import tempfile
 import unittest
@@ -8,6 +10,7 @@
 from unittest import mock
 
 import base_cli
+from base_cli._runtime import prune_log_files
 from base_cli.testing import invoke
 
 
@@ -18,6 +21,39 @@ def write_log_file(path: Path, mtime: int) -> None:
 
 
 class AppLogRetentionTests(unittest.TestCase):
+    def test_ignores_stale_paths_in_retention_index(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            log_dir = Path(tmpdir) / "runs" / "seed" / "logs"
+            old_a = log_dir / "20260620T120000_a.log"
+            old_b = log_dir / "20260621T120000_b.log"
+            old_c = log_dir / "20260622T120000_c.log"
+            current = log_dir / "20260623T120000_current.log"
+            phantom = log_dir / "deleted" / "phantom.log"
+            for path, mtime in ((old_a, 1), (old_b, 2), (old_c, 3)):
+                write_log_file(path, mtime)
+            (log_dir / ".base-cli-log-index.json").write_text(
+                json.dumps(
+                    {
+                        "version": 1,
+                        "logs": [str(path.resolve()) for path in (old_a, old_b, old_c, phantom)],
+                    }
+                ),
+                encoding="utf-8",
+            )
+
+            prune_log_files(log_dir, current, 3, logging.getLogger(__name__))
+
+            self.assertFalse(old_a.exists())
+            self.assertTrue(old_b.exists())
+            self.assertTrue(old_c.exists())
+            current.write_text("current log\n", encoding="utf-8")
+            self.assertEqual(len(tuple(log_dir.rglob("*.log"))), 3)
+            index = json.loads((log_dir / ".base-cli-log-index.json").read_text(encoding="utf-8"))
+            self.assertEqual(
+                {Path(path) for path in index["logs"]},
+                {old_b.resolve(), old_c.resolve(), current.resolve()},
+            )
+
     @unittest.skipUnless(importlib.util.find_spec("click"), "Click is not installed")
     def test_uses_retention_index_after_initial_discovery(self) -> None:
         app = base_cli.App(name="retention-index", max_log_files=2)