first check the clear caulk, just because its clear doesn't mean that its not paintable. If its not paintable then the only thing you can do is to remove the caulk.

If it's 100% silicone caulk, you will need a paint scraper to remove it. Very simple once it's cured. You may have to sand a wee bit to get the crumbs off the margins. Priming again with some high-adhesion primer (oil or shellac-base) may be in order, but really only if you notice the paint start to "fisheye" (being repelled by the silicone).
Casey

Thank you for the advice, I removed the caulk and all is well.

Larrilee