diff --git a/hgext/largefiles/lfutil.py b/hgext/largefiles/lfutil.py
--- a/hgext/largefiles/lfutil.py
+++ b/hgext/largefiles/lfutil.py
@@ -430,6 +430,7 @@ def composestandinmatcher(repo, rmatcher
     def composedmatchfn(f):
         return isstandin(f) and rmatcher.matchfn(splitstandin(f))
 
+    smatcher._was_tampered_with = True
     smatcher.matchfn = composedmatchfn
 
     return smatcher
@@ -716,6 +717,7 @@ def updatestandinsbymatch(repo, match):
         return match
 
     lfiles = listlfiles(repo)
+    match._was_tampered_with = True
     match._files = repo._subdirlfs(match.files(), lfiles)
 
     # Case 2: user calls commit with specified patterns: refresh
@@ -746,6 +748,7 @@ def updatestandinsbymatch(repo, match):
     # user.  Have to modify _files to prevent commit() from
     # complaining "not tracked" for big files.
     match = copy.copy(match)
+    match._was_tampered_with = True
     origmatchfn = match.matchfn
 
     # Check both the list of largefiles and the list of
diff --git a/hgext/largefiles/reposetup.py b/hgext/largefiles/reposetup.py
--- a/hgext/largefiles/reposetup.py
+++ b/hgext/largefiles/reposetup.py
@@ -181,6 +181,7 @@ def reposetup(ui, repo):
                     return newfiles
 
                 m = copy.copy(match)
+                m._was_tampered_with = True
                 m._files = tostandins(m._files)
 
                 result = orig(
@@ -193,6 +194,7 @@ def reposetup(ui, repo):
                         dirstate = self.dirstate
                         return sf in dirstate or dirstate.hasdir(sf)
 
+                    match._was_tampered_with = True
                     match._files = [f for f in match._files if sfindirstate(f)]
                     # Don't waste time getting the ignored and unknown
                     # files from lfdirstate