I'm in the same boat as dubbyjig, only mine isn't to the mushroom stage yet. I had the windows out of our previous RVs which were wood frame TCs. Those just had screws that went into the wood frame, but from what Motor7 says his Flair is a bit different. Do the inner and outer window sections just clamp together? I haven't had mine out yet ('93 26' Flair) but I'm headed in that direction. The drivers side appears to have a slight bubble just behind it.
The windows I've removed from the TCs I did about like Motor7, except I screwed the few left in place out a small amount to allow the window a bit of movement there. I was able to do them by myself, but they may have been different (smaller?).
I have several side doors off resealing them and they are attached with self tapping sheet metal screws that go into the metal frame. Some of these break break off if rusted. I've been replacing them with stainless screws. For the broken screws I'm planning to use stainless self tapping. I removed the trim covering them with a long narrow screwdriver. If bent too much it will break, but can be bought in long strips at a place that sells RV parts.
I've been using plastic scrapers, that I think were intended to remove auto interior trim, from Harbor Freight to get windows off and remove the excess putty to avoid scratching paint. It works most of the time, and they are cheap.
I like butyl tape a lot better than the putty type.
I also found wood preservative and wood hardener at Home Depot. I've been applying the preservative to any exposed wood I find that is sound and any new wood that I add. I've used the hardener on wood that is still sound with some deterioration and will be difficult to replace. This is not for interior or decorative wood, only wood that is or could be exposed to the elements.
One more thing, If you remove windows with sections that roll out be sure to remove the handles from the inside or, like me, you will be replacing them.:-))
Best of luck.