diff --git a/src/borg/crypto/file_integrity.py b/src/borg/crypto/file_integrity.py
index 87518a2a7..76503057f 100644
--- a/src/borg/crypto/file_integrity.py
+++ b/src/borg/crypto/file_integrity.py
@@ -127,6 +127,7 @@ def __init__(self, path, write, filename=None, override_fd=None, integrity_data=
         self.writing = write
         mode = 'wb' if write else 'rb'
         self.file_fd = override_fd or open(path, mode)
+        self.file_opened = override_fd is None
         self.digests = {}
 
         hash_cls = XXH64FileHashingWrapper
@@ -189,9 +190,13 @@ def hash_part(self, partname, is_final=False):
 
     def __exit__(self, exc_type, exc_val, exc_tb):
         exception = exc_type is not None
-        if not exception:
-            self.hash_part('final', is_final=True)
-        self.hasher.__exit__(exc_type, exc_val, exc_tb)
+        try:
+            if not exception:
+                self.hash_part("final", is_final=True)
+            self.hasher.__exit__(exc_type, exc_val, exc_tb)
+        finally:
+            if self.file_opened:
+                self.file_fd.close()
         if exception:
             return
         if self.writing:
diff --git a/src/borg/repository.py b/src/borg/repository.py
index 56c846480..61905b394 100644
--- a/src/borg/repository.py
+++ b/src/borg/repository.py
@@ -613,7 +613,7 @@ def flush_and_sync(fd):
             os.fsync(fd.fileno())
 
         def rename_tmp(file):
-            os.rename(file + '.tmp', file)
+            os.replace(file + ".tmp", file)
 
         hints = {
             b'version': 2,
@@ -1358,13 +1358,12 @@ def get_segments_transaction_id(self):
     def cleanup(self, transaction_id):
         """Delete segment files left by aborted transactions
         """
+        self.close_segment()
         self.segment = transaction_id + 1
         count = 0
         for segment, filename in self.segment_iterator(reverse=True):
             if segment > transaction_id:
-                if segment in self.fds:
-                    del self.fds[segment]
-                safe_unlink(filename)
+                self.delete_segment(segment)
                 count += 1
             else:
                 break
diff --git a/src/borg/testsuite/repository.py b/src/borg/testsuite/repository.py
index c52820e33..c51574920 100644
--- a/src/borg/testsuite/repository.py
+++ b/src/borg/testsuite/repository.py
@@ -720,7 +720,7 @@ def corrupt_object(self, id_):
             fd.write(b'BOOM')
 
     def delete_segment(self, segment):
-        os.unlink(os.path.join(self.tmppath, 'repository', 'data', '0', str(segment)))
+        self.repository.io.delete_segment(segment)
 
     def delete_index(self):
         os.unlink(os.path.join(self.tmppath, 'repository', f'index.{self.get_head()}'))
@@ -1002,6 +1002,14 @@ def test_crash_before_compact(self):
         # skip this test, we can't mock-patch a Repository class in another process!
         pass
 
+    def test_repair_missing_commit_segment(self):
+        # skip this test, files in RemoteRepository cannot be deleted
+        pass
+
+    def test_repair_missing_segment(self):
+        # skip this test, files in RemoteRepository cannot be deleted
+        pass
+
 
 class RemoteLoggerTestCase(BaseTestCase):
     def setUp(self):