Hello Lorsar,
Personally I think the rcommendation of JohnK works out best.
I would not use body filler to replace the missing material. That would turn out to be too solid or stiff and can crack when the two lock pins of the softtop frame come too close to the repair area if the softtop isn't aligned superbly. I would rather recommend using a semisoft material - foamy for instance - very much as the original material is. Always try to repair with the same type of material your work area is composed of. Maybe the black window sealant (semisolid rubber-like sealant) would also work well.
Finally, I would repair this with liquid leather or leather crack filler - see the products of leatherique.com or equivalent.
Personally I think the recommendation of JohnK with recovering with new vinyl after adequately filling will work out best.
Achim
