Thanks all. Using butyl makes sense. They sell it as "tape" (like a flexible dowel) which I've used for other things before, or you can get it in a caulk tube.
At this point I think I'm leaving the seal alone. Also it's a single seal so I would have to pull both sides of the glass to replace it. That being said, I think I'll pull the glass, make sure the groove is good and clean, and replace it with no sealant. If I have any issues after that I can put some butyl caulk in there.
My price on the glass is $970. The price to have the shop do it is $2000. I'm doing it myself.
"People who spend their time telling others what can't be done only annoy those of us out there doing it!"