New York, Pennsylvania, Federal charges are all separate by the sounds of it.

Mangione's Pennsylvania lawyer Thomas Dickey was preparing to blame the Commonwealth of Pennsylvania that he is stuck in New York and can't appear in Pennsylvania court. Delays of bringing his client to the courtroom, which if it doesn't begin within 365 days for reasons caused by the Commonwealth's failure to exercise due diligence, is grounds for filing for dismissal of the Pennsylvania charges he was initially arrested on, according to his lawyer's memos.

(ETA: His lawyer has other strategies too, obviously. Many related to the constitutionality of his arrest at the McDonald's)