Sounds like the channel is acting as a chip guard protector for the edge of the glass. That edge is always on the inside of the fixed pane. Just a few areas of clear caulk in the bottom of the channel will be sufficient. By a few areas I mean a small area of caulk at each end and a couple of areas towards the center. Don't over do it with continuous caulking. The channel should not be almost impossible to remove because potentially it could be put onto a new piece of glass should that pane ever get broken.
I myself might choose to get a small tube of Lexel for the job if you don't have use for a big supply of caulk. The reason for choosing Lexel is that it is handy to have in your emergency on the road repair kit. It is not silicone based, it does work with glass,
fiberglass, vinyl, rubber and aluminum. It will stick to damp surfaces which is why it is just right for an emergency repair kit if you get a leaky spot in a rain storm. It is crystal clear and it dries quickly. The tube of material can even go through freezing and still be used afterwards. It does come in small squeeze tubes.
Sold at local hardware stores and at big box Home Center stores most everywhere. They advertise it as the duct tape of caulks
http://www.sashco.com/products/lexel/
Linear Mode
