||When you change the name of a mailbox Poco will update the filters but deleting one does not. I wouldn't want it to either (although perhaps with a confirmation prompt that would be ok), typically I would be going in to change the filters myself in this case.
The mailbox will be recreated the next time the filter encounters a message meeting the criteria. You will be able to see recreated mailbox only after refreshing the mailboxes pane. Therefore it is better to manually delete or update the filter, otherwise you are back where you were before deleting. :)