Awhile ago I had problems with my rear zipper and did a fix that doesn't use the rear zipper. I'm sure a few out there will hate the way it looks, but its so awesome.
I had a sewing shop sew Velcro to the rear window, and used the sticky side of the Velcro on the fabric that is attached to the vehicle. you can see the sewing string near my middle finger in the pic.
It doesn't seal 100 percent, but it does what it should and last winter wasn't a problem.
The top is held up by big ass binder clips. I figured it wouldn't hurt to slice my soft top since I was almost going to get a new one.
These clips are pretty heavy duty and I have only switched them out once or twice.
I also keep them in when the back window is down.
I know it looks pretty whacky, and yeah yeah yeah.... Soft tops have had zippers for years and worked well.
I did this as a temporary fix and decided not to buy another soft top. It literally takes me like 8 seconds, no exaggeration, to put the window down and 15 seconds to put it back up. I put it up and take it down often and it makes way easier.
I have a bedlined interior so if water gets in its not that big of a deal. I travel with a guitar and laptop often and don't worry about the rain, even at 70 miles on the highway not that much comes in even though there are small gaps in between the binder clips when the window is propped up.
When the winter rolls around, I have some kind of soft, sticky weather stripping that I can line the gaps with on the inside since I won't be taking the back window out as much and I rarely haul big items that require the rear rollbar and window to come out. It will seal it better but its probably not necessary since the jeep heater is awesome
Can provide more info if needed!