Will a new flood coat fill bubble holes and divots in cured epoxy?

Only once the bubbles themselves are sanded out. A fresh coat fills sanding scratches and shallow low spots, but it does not fix bubbles still trapped in the cured layer underneath. You have to sand down until they are gone; how far varies from project to project, so start with a coarse grit if you need to remove a lot of material or open the bubbles up.

After that, the pits and divots the bubbles leave behind do not need to be pre-filled with epoxy. Sand them out as well as you can and make sure no divot or imperfection is more than 1/8" in height difference. UltraClear Bar & Table Top Epoxy self-levels at 1/8" per flood coat, so anything under that levels out in the new pour. Finish the entire surface with 220-320 grit, wipe the dust off with acetone or denatured alcohol, let it dry, and re-pour the flood coat.

You do not have to sand down to bare wood. Remove only enough to get rid of the bubbles; if a full layer of epoxy remains, pour straight over it. If sanding exposes wood, seal coat that area first or the new flood coat will bubble again.

For a few small holes in an otherwise finished piece, the filler is the same epoxy: sand and clean the spots, then brush a small, well-mixed batch over them with an artist's brush. The patch may not blend seamlessly; a full re-pour is the only seamless fix.