diff --git a/mercurial/merge.py b/mercurial/merge.py
--- a/mercurial/merge.py
+++ b/mercurial/merge.py
@@ -741,7 +741,15 @@ def applyupdates(repo, actions, wctx, mc
 
     numupdates = sum(len(l) for m, l in actions.items() if m != 'k')
 
+    def dirtysubstate():
+        # mark '.hgsubstate' as possibly dirty forcibly, because
+        # modified '.hgsubstate' is misunderstood as clean,
+        # when both st_size/st_mtime of '.hgsubstate' aren't changed,
+        # even if "submerge" fails and '.hgsubstate' is inconsistent
+        repo.dirstate.normallookup('.hgsubstate')
+
     if [a for a in actions['r'] if a[0] == '.hgsubstate']:
+        dirtysubstate()
         subrepo.submerge(repo, wctx, mctx, wctx, overwrite)
 
     # remove in parallel (must come first)
@@ -760,6 +768,7 @@ def applyupdates(repo, actions, wctx, mc
     updated = len(actions['g'])
 
     if [a for a in actions['g'] if a[0] == '.hgsubstate']:
+        dirtysubstate()
         subrepo.submerge(repo, wctx, mctx, wctx, overwrite)
 
     # forget (manifest only, just log it) (must come first)
@@ -785,6 +794,7 @@ def applyupdates(repo, actions, wctx, mc
         z += 1
         progress(_updating, z, item=f, total=numupdates, unit=_files)
         if f == '.hgsubstate': # subrepo states need updating
+            dirtysubstate()
             subrepo.submerge(repo, wctx, mctx, wctx.ancestor(mctx),
                              overwrite)
             continue
diff --git a/tests/test-subrepo.t b/tests/test-subrepo.t
--- a/tests/test-subrepo.t
+++ b/tests/test-subrepo.t
@@ -758,6 +758,8 @@ test if untracked file is not overwritte
 
   $ echo issue3276_ok > repo/s/b
   $ hg -R repo2 push -f -q
+  $ touch -t 200001010000 repo/.hgsubstate
+  $ hg -R repo status --config debug.dirstate.delaywrite=2 repo/.hgsubstate
   $ hg -R repo update
   b: untracked file differs
   abort: untracked files in working directory differ from files in requested revision (in subrepo s)
@@ -766,6 +768,7 @@ test if untracked file is not overwritte
   $ cat repo/s/b
   issue3276_ok
   $ rm repo/s/b
+  $ touch -t 200001010000 repo/.hgsubstate
   $ hg -R repo revert --all
   reverting repo/.hgsubstate (glob)
   reverting subrepo s