diff --git a/hgext/largefiles/overrides.py b/hgext/largefiles/overrides.py
--- a/hgext/largefiles/overrides.py
+++ b/hgext/largefiles/overrides.py
@@ -1785,7 +1785,9 @@
         # mark all clean largefiles as dirty, just in case the update gets
         # interrupted before largefiles and lfdirstate are synchronized
         for lfile in oldclean:
-            lfdirstate.normallookup(lfile)
+            entry = lfdirstate._map.get(lfile)
+            assert not (entry.merged_removed or entry.from_p2_removed)
+            lfdirstate.set_possibly_dirty(lfile)
         lfdirstate.write()
 
         oldstandins = lfutil.getstandinsstate(repo)