When we painted our bus there wasn't any silicone around the windows. If you have a long time to get it done, I'd say test paint the silicone and let it dry a couple weeks then see if it peels off easily. If it doesn't, then just go ahead and paint over it. If you have any leaks, though, just go ahead and redo all the caulk. You can hand sand it with 320 or higher grit, but an electric or air sander makes it a lot easier. It doesn't take much, just a scuff, but it's a lot of area to cover. Make sure to wash it good first. We probably had over 100 hours of prep work for painting, because our clear coat was 50% peeled off and we had to go over the entire bus with razor scrapers to remove it all. It was like a peeling sunburn.
My build thread:http://www.skoolie.net/forums/f11/build-thread-for-haulin-oats-and-goats-11237.html#post113500
A gal, a guy, three cats, two dogs, one rabbit, and one goat, traveling the country together.