At the moment there isn't a way to add multiple Accounts to a Booking, and then select which one to use on a Document. There is, however, a workaround using Locked Documents.

What you would have to do is ensure the Documents with the 'old' company are Locked. This happens automatically when you send a Document to a guest, or you can manually do it by marking it as sent or completed.

Locking a document means you can then make changes to a Booking without affecting those Documents. You'd then update your Booking with the new company info & create your new Document/s as needed.