I have had this issue now for a couple years, The problem off course is the car side zipper's stitching is coming apart and in my case many of the stitches have made the holes long or a tear, this means that you can not reuse the hole and must add more stitching to fix it.
This works for a bit, a season if you will. After that the repair stitching becomes even more radical and non-uniform and since you have to go around existing holes and have a firm surface to stitch in, the tension on the window can increases and causes more stitches to come loose or broken. The more you put the top up and down the worse it gets.
In my mind now the real solution is a new top. Until you I that, I have to do this year after year and your my baby is going to look worse and worse.
You can take the top off and repair it, but this costs maybe up to half of what a new top costs if you cant do it yourself.
I plan to get a new top this year, I am tired of this half-ass repair.