I've used fabric paint to paint stars and moons that glow in the dark in my daughter's bedroom. She has outgrown the bedroom and we are now in the process of redoing it. Unfortunately, the fabric paint is raised and sanding it down doesn't help. I've also tried paint thinner but that doesn't seem to help either. Any ideas because painting over these would just look like poop.

Have you tried using some drywall tape over the areas that need it then level it out with drywall compound? You may end up skinning the entire ceiling depending on how bad the surface is. Then seal, prime and paint.