diff --git a/mercurial/filemerge.py b/mercurial/filemerge.py
--- a/mercurial/filemerge.py
+++ b/mercurial/filemerge.py
@@ -666,6 +666,11 @@
         onfailure = _("merging %s failed!\n")
         precheck = None
 
+        # Must flush any deferred contents if running an external merge tool.
+        from . import context
+        if isinstance(wctx, context.overlayworkingctx):
+            wctx.flushall()
+
     toolconf = tool, toolpath, binary, symlink
 
     if mergetype == nomerge: