What you need is a barrier coat of some sort. The epoxy is fine to sand, they use terms like "non-sanding" but it only means it doesn't HAVE to be sanded, not that it CAN'T be sanded.
Now, if you mix it as a "non-sanding" sealer you are adding more reducer.......just what you don't want. You want to spray it as a primer, spray it kinda dry over those sanded thru areas. Spray a coat and let it set good to flash off before you follow with more coats. After a few you have created a barrier coat over that sensitive area.
You then sand it and the surrounding area and you are good to go with base and clear.