Are you saying that after the screen was repaired that the pen did not work? Or did the pen work for a while after the repair and then stop?
If it never worked after the repair, you need to contact Microsoft and have them handle this. If it worked for a while after the repair, can you try your pen on someone else's Surface and their pen on yours to diagnose?
Note that pens do not need to be paired to write, so the bluetooth functions may continue to work to open apps etc.