diff --git a/mercurial/upgrade_utils/engine.py b/mercurial/upgrade_utils/engine.py
--- a/mercurial/upgrade_utils/engine.py
+++ b/mercurial/upgrade_utils/engine.py
@@ -412,7 +412,35 @@
     """
     # TODO: don't blindly rename everything in store
     # There can be upgrades where store is not touched at all
-    util.rename(currentrepo.spath, backupvfs.join(b'store'))
+    backupstorevfs = vfsmod.vfs(backupvfs.join(b'store'))
+    util.makedirs(backupstorevfs.base)
+    for path, kind, st in sorted(currentrepo.store.vfs.readdir(b'', stat=True)):
+        # Skip transaction related files.
+        if path.startswith(b'undo'):
+            continue
+        # Only copy regular files.
+        if kind != stat.S_IFREG:
+            continue
+        # Skip other skipped files.
+        if path in (b'lock',):
+            continue
+        src = currentrepo.store.rawvfs.join(path)
+        dst = backupstorevfs.join(path)
+        util.copyfile(src, dst, copystat=True)
+    if currentrepo.svfs.exists(b'data'):
+        util.copyfiles(
+            currentrepo.svfs.join(b'data'),
+            backupstorevfs.join(b'data'),
+            hardlink=False,
+        )
+    if currentrepo.svfs.exists(b'meta'):
+        util.copyfiles(
+            currentrepo.svfs.join(b'meta'),
+            backupstorevfs.join(b'meta'),
+            hardlink=False,
+        )
+
+    currentrepo.vfs.rmtree(b'store', forcibly=True)
     util.rename(upgradedrepo.spath, currentrepo.spath)
 
 
@@ -512,10 +540,4 @@
     )
     scmutil.writereporequirements(srcrepo, upgrade_op.new_requirements)
 
-    # The lock file from the old store won't be removed because nothing has a
-    # reference to its new location. So clean it up manually. Alternatively, we
-    # could update srcrepo.svfs and other variables to point to the new
-    # location. This is simpler.
-    backupvfs.unlink(b'store/lock')
-
     return backuppath
diff --git a/tests/test-upgrade-repo.t b/tests/test-upgrade-repo.t
--- a/tests/test-upgrade-repo.t
+++ b/tests/test-upgrade-repo.t
@@ -592,10 +592,6 @@
   data
   fncache
   phaseroots
-  undo
-  undo.backup.fncache
-  undo.backupfiles
-  undo.phaseroots
 
 unless --no-backup is passed