diff --git a/hgext/rebase.py b/hgext/rebase.py
--- a/hgext/rebase.py
+++ b/hgext/rebase.py
@@ -447,11 +447,11 @@
             if dest.closesbranch() and not self.keepbranchesf:
                 self.ui.status(_(b'reopening closed branch head %s\n') % dest)
 
-        self.prepared = True
-
         # Calculate self.obsolete_* sets
         self._handleskippingobsolete()
 
+        self.prepared = True
+
     def _assignworkingcopy(self):
         if self.inmemory:
             from mercurial.context import overlayworkingctx
@@ -2192,7 +2192,6 @@
     obsolete_with_successor_in_destination = {}
     obsolete_with_successor_in_rebase_set = set()
 
-    assert repo.filtername is None
     cl = repo.changelog
     get_rev = cl.index.get_rev
     extinctrevs = set(repo.revs(b'extinct()'))