I think you should try a skin coat and hope for the best, but I'm not optimistic. In the places where I sanded through enough to see a white grid of fiberglass fibers, that grid has remained visible. But a few scattered blemishes won't be enough to mar the beauty of a bright finish.

Apply the skim coat and then make your decision.

   After adding the coat, the white fibers are gone... Now to more sanding... Only handsanding this time though!

When the epoxy gets thin, the light that's being piped along the length of the fibers leaks out because you don't have enough material to cause a large enough change in refractive index to effect a total internal reflection, so the fibers become visible even though you haven't broken them yet.

Wetting the surface with denatured alcohol temporarily makes the fibers go away because that adds enough material to restore the change in the refractive index and the light stays inside the fibers. Once the alcohol evaporates, the fibers become visible again. 

So the next time this happens, just rub the surface down with a rag dampened with alcohol. If the fibers go away, you're fine. Just stop sanding and put on another layer of epoxy, exactly what you did this time. If the alcohol doesn't make the fibers go away, then save your epoxy. No amount of recoating will make the threads go away, they are now a permanent part of your finish. Either cover them with paint, a rice paper graphic, an onlay, etc. or tell everyone they're the deliberate imperfection you put in to show that you are not guilty of hubris.

Have fun,

Laszlo