When that happened on my YJ, I would just use some spray lube on the zipper and get a little aggressive trying to run it past the bad spot using a pair of pliers to push the zipper. However, it was a pretty weathered top on a trail rig so I didn't worry about hurting it.
Make sure there is no tension along either side of the zipper. You may need to partially remove the top. Lubricate the zipper generously on both sides, and then give it a shot un-zipping it. Try to fully unzip it. You may have to realign the zipper teeth once you have it unzipped.
I had to do this with my CJ8 when I first bought it. I got that problem zipper fixed and it's been good for almost 2 years since.
Lube is your friend. If you can get a silicone lubricant with higher temperatures, like letting the top sit in the sun for a couple of hours to make the material more malleable, you're going to be able to work that zipper through the separated part. Be gentle at first but sometimes it takes a more aggressive approach. The trick is to get the slack out of the one side. If you can pull on the loose side stronger that the taught side while working the zipper through the separated spot it will go more smoothly. Be patient.