did you make changes with respect to linked tables? Perhaps the db is attempting to resolve a link in a new table and cannot for some reason. Methinks the table links will be resolved regardless of your shift key property setting, although whether or not a user has rights to a table won't be resolved until the user attempts anything that accesses it. That might be immediately if startup code is attempting access data to (for example, validate a user).
Can you open the be by itself without any issues/warnings? If so, can you open all the linked tables in the be?
If yes, then perhaps your attempt to alter the shift bypass property wasn't successful, or you actually forgot to do it.
In those cases, you'd need to write code in a new db to set the property in the target db.
The more we hear silence, the more we begin to think about our value in this universe.
Paraphrase of Professor Brian Cox.