FYI, I was able to successfully remove the cross storage reference in the root of my main Zope database by explicitly setting the missing database connection to a hacked DummyConnection instance. I probably could have dug deeper to create a real connection, but this worked. from ZODB import FileStorage, DB import transaction storage = FileStorage.FileStorage('Data.fs') app = DB(storage).open().root()['Application'] base_conn = app._p_jar class DummyConnection: """ implements enough of a connection to allow for removing of the cross database reference """ def __init__(self): self.connections = [] self._cache = {} def get(self, key): return None def open(self, **kw): return DummyConnection() base_conn._db.databases['site1'] = DummyConnection() app._objects = tuple([i for i in app._objects if i['id'] != 'badID']) transaction.get().commit() It's quite the hack, but allowed us to get the database back. Brian Brinegar Web Services Coordinator Engineering Computer Network -- Brian Brinegar Web Services Coordinator Engineering Computer Network