Same thing happened to me a couple seasons back. Had Chris from Rovertek (amazing guy) take it to a marine repair guy. Easy fix, couple hundred and it looks great. Look for a marine/boat repair shop as they work with the exact type of windows that our soft tops have.
I did the same thing last winter, cost was $100 and they also stitched in middle straps to keep the rolled up sides from sagging. Winter is a good time for this, the boat shops aren't busy and are happy to have the business.