That seal is just a cosmetic trim piece. Remove it and the glass will still be there. I've had mine out a few times.
If you are worried about it, take it out, start at the bottom to make sure you have a good fit, then work it around so the gap is at the top. Just make sure not to stretch the seal when you put it back in.
You do need to make sure the weep holes aren't clogged though.
Also, the caulking around the outside of the window is more cosmetic and only provides sealing until it shrinks or cracks. The true seal is the putty between the camper and the window. What usually happens is they cut the window opening a bit on the large size so that when the window is put in place, there is very little overlap at the top. When you put the window back in, make sure to shim it up so the window is cengtered in the opening.