diff --git a/mercurial/merge.py b/mercurial/merge.py
--- a/mercurial/merge.py
+++ b/mercurial/merge.py
@@ -1111,6 +1111,10 @@
 
     _warnifmissingcwd(repo, cwd)
 
+    # It's necessary to flush here in case we're inside a worker fork and will
+    # quit after this function.
+    wctx.flushall()
+
 def batchget(repo, mctx, wctx, actions):
     """apply gets to the working directory
 
@@ -1146,6 +1150,10 @@
     if i > 0:
         yield i, f
 
+    # It's necessary to flush here in case we're inside a worker fork and will
+    # quit after this function.
+    wctx.flushall()
+
 def applyupdates(repo, actions, wctx, mctx, overwrite, labels=None):
     """apply the merge action list to the working directory
 
@@ -1214,6 +1222,10 @@
         progress(_updating, z, item=item, total=numupdates, unit=_files)
     removed = len(actions['r'])
 
+    # We should flush before forking into worker processes, since those workers
+    # flush when they complete, and we don't want to duplicate work.
+    wctx.flushall()
+
     # get in parallel
     prog = worker.worker(repo.ui, 0.001, batchget, (repo, mctx, wctx),
                          actions['g'])