My brother had a couple of spots on one door where the clear coat was failing. The big spot was right along the window molding, we removed the molding, taped at the body pinstripe and sanded all of the good clear coated area with 320. In the area where the clear was gone we were very careful with the prep, get it clean and remove any loose material, but the lower paint coats are relatively fragile and too much prep will change the color. We used some fine steel wool and lacquer thinner, most of the loose, flaking clear was first removed by scraping with my thumb nail.
The other spot was at the edge on a body line, like someone was too aggressive with the buffer and removed the clear in a small area. We prepped and back taped, that small area, 1.5" x .5". To back tape, fold about 1/4" of a piece of 1" over so that the adhesive side is up, stick the 3/4" sticky side to the body, then adjust the 1/4" flap so that it's about 3/16" off the body. This makes a tapered edge on the new paint, making it much easier to blend.
Sprayed it with Krylon industrial clear that we got at an auto paint store, about 4 good coats. Came out very nice, there is some discoloration in the area where the clear was missing for the longest, it looks much better. Will see how long it holds up, but it's much better than the missing clear coat and probably greatly extended the usable life of the paint job.
Like any paint job the key is prep, the area must be clean of any wax, etc. Anywhere that the paint is going the shine must be removed, sandpaper, scotch bright, steel wool, etc. If the new paint doesn't have tooth to stick to it will peal, flake off, looking as bad or worse than before.