diff -r 0d6b3572ad92 -r a580b2d65ded hgext/rebase.py
--- a/hgext/rebase.py	Wed May 17 09:43:50 2017 -0700
+++ b/hgext/rebase.py	Thu May 18 13:18:05 2017 -0700
@@ -420,6 +420,11 @@
                                            editor=editor,
                                            keepbranches=self.keepbranchesf,
                                            date=self.date)
+                    if newnode is None:
+                        # If it ended up being a no-op commit, then the normal
+                        # merge state clean-up path doesn't happen, so do it
+                        # here. Fix issue5494
+                        mergemod.mergestate.clean(repo)
                 else:
                     # Skip commit if we are collapsing
                     repo.dirstate.beginparentchange()