The BPA (and at least some other lawful entities) do not consider the loss of your ship to absolve you of all guilt. I do need to get the RP done with Cryer| concerning your crimes, but until that time or whenever you pay your outstanding fines in-game, you will remain a criminal. Even if you RP some "the last guy died but I have his ship" stuff.
You may wish to consult the following chart, courtesy of the BPA: