diff --git a/apps/server/src/pullRequest/PullRequestReadCache.test.ts b/apps/server/src/pullRequest/PullRequestReadCache.test.ts
index a6a14dbae9cabd7d6b8d1ddff5e98058d9edd3bc..f1b543d1eddf334b713afd0cca4f417594a84e31 100644
--- a/apps/server/src/pullRequest/PullRequestReadCache.test.ts
+++ b/apps/server/src/pullRequest/PullRequestReadCache.test.ts
@@ -44,18 +44,21 @@ it.layer(NodeServices.layer)("PR filesystem cache", (it) => {
       );
       const unrelated = "unrelated.json";
       yield* fs.writeFileString(`${directory}/${unrelated}`, "{}");
+      // Starts with the store id but is not an entry file.
+      const prefixed = "pr-v2-backup.json";
+      yield* fs.writeFileString(`${directory}/${prefixed}`, "{}");
       const justExpired = Duration.sum(
         PullRequestReadCache.ENTRY_FILE_MAX_AGE,
         Duration.seconds(1),
       );
-      yield* ageFiles(directory, [stale!, revisions!, unrelated], justExpired);
+      yield* ageFiles(directory, [stale!, revisions!, unrelated, prefixed], justExpired);
       yield* ageFiles(directory, [fresh!], PullRequestReadCache.ENTRY_FILE_MAX_AGE);
 
       yield* PullRequestReadCache.pruneExpiredEntryFiles(directory);
 
       assert.deepStrictEqual(
         (yield* fs.readDirectory(directory)).toSorted(),
-        [fresh!, revisions!, unrelated].toSorted(),
+        [fresh!, revisions!, unrelated, prefixed].toSorted(),
       );
     }),
   );
diff --git a/apps/server/src/pullRequest/PullRequestReadCache.ts b/apps/server/src/pullRequest/PullRequestReadCache.ts
index a691898769be43101636062e00e5212f66da03de..a749a14031fd36c8b675809af9264be158d38bb3 100644
--- a/apps/server/src/pullRequest/PullRequestReadCache.ts
+++ b/apps/server/src/pullRequest/PullRequestReadCache.ts
@@ -27,6 +27,8 @@ const CONCURRENT_READS = 512;
 // Persistence prefixes every entry key with the store id, so each entry file
 // name starts with it. The scope `revisions` file does not.
 const STORE_ID = "pr-v2";
+// An entry file is the store id followed by the SHA-256 hex digest of its key.
+const ENTRY_FILE_NAME = new RegExp(`^${STORE_ID}[0-9a-f]{64}$`);
 /**
  * Entries expire a minute after they are written, and a write sets the file's
  * mtime. A file untouched for a day is long expired; the day only leaves slack
@@ -186,7 +188,7 @@ export const pruneExpiredEntryFiles = Effect.fn("PullRequestReadCache.pruneExpir
     const path = yield* Path.Path;
     const cutoff = (yield* Clock.currentTimeMillis) - Duration.toMillis(ENTRY_FILE_MAX_AGE);
     const entries = (yield* fileSystem.readDirectory(directory)).filter((name) =>
-      name.startsWith(STORE_ID),
+      ENTRY_FILE_NAME.test(name),
     );
     // One file at a time, and `partition` visits every file, so one locked file
     // does not stop the sweep.