Really, you are suggesting leave the chips on there, stuck on the rubber? Re-gluing down with those chips between rubber and new roof would at best look like crap, cant see how you could walk on it without eventually puncturing, let alone getting it to bond. Any appurtenance near like vent etc would be difficult to seal.
Myself I wouldn't trust the membrane after pulling up, whole point of this was to fix water damage, thats just me. If able to clean enough and comfortable thats membranes undamaged I assumed OP was regluing down. Dont know where he is on this project.. no update on either of the threads its in..