diff --git a/mercurial/merge.py b/mercurial/merge.py
--- a/mercurial/merge.py
+++ b/mercurial/merge.py
@@ -1699,6 +1699,7 @@
             repo.vfs.write('updatestate', p2.hex())
 
         stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels)
+        wc.flushall()
 
         if not partial:
             with repo.dirstate.parentchange():