A lot of the stuff in the backlot was rotting. What wasn't, will probably go in storage One exception might be the few Star Wars items (if I recall, part of skiff and/or snow speeder?). I would hope they would be restored and added to SWL.
As to what is within GMR, I believe most of the queue stuff was on extended loan from collectors. The authentic costumes Disney does own will likely go in storage or be shifted around (perhaps to DCA or WDS). But all in all, there isn't really anything notable inside the ride itself AFAIK (as the Casablanca myth has been thoroughly debunked).