It doesn't matter if the fare is no longer available... when rebooking the system is supposed to keep your old fare basis, and even if they do it manually they are supposed to save that basis into the new ticket.

Also to note, if an agent does it quick/sloppy and just sticks you in the lowest available bucket, say T, the system will still have your previous fare basis which is what it uses to determine eligibility for things like seat selection etc.