Aye, unless they have a reason (i.e. ban, suspensions, bad behavior etc.) they shouldn't delete your pirate.
So if you have not had any problems with behavior and such, then your pirate should be there. Best to
take Bart's advice and contact Disney.
Edit: And no, the 2 week pass should have nothing to do with the loss of your pirates. Most likely an error on Disney's part.
Welcome back though!