I have done quite a few tops and i do not see any way to replace these and save the old top it would be quite a project and the top is probably brittle by now and would probably rip but best of luck if you try Steve
If your top is good, either the pads were not replaced when the top was installed or they are poor material. As stated above, correct replacement requires removing the top.
You can probably cover the pads and shield them from further rub (on the bows) damage by carefully cutting black material to fit between the header bow and the bow above the rear window. The material should tuck in above the pads too - at least a few inches.
Black 3m weatherstrip adhesive (a.k.a. liquid duct tape) will hold the material to the black pad at the edge of the front bow and the edge of the bow above the rear window. I would also put a small spot between the edge of the material tucked above the pad and the top of the pad.
Inexpensive top pad material can be bought from JCWhitney. Don't overdo the 3M adhesive. It would also be a good idea to mask the edge of the header bow and the bow above the rear window, in case you get adhesive on them. Working overhead in a confined space, it may also be a good idea to wear ovealls and cover the seats - cause stuff happens.