I too have used epoxy for many years to fill small hold in stone
surfaces. Don't expect it to work on anything over a mm or so though.
On those larger holes, use Opticon which is a resin.
When polishing surfaces with small pits/holes filled with epoxy, I
usually go though my normal routine of working up to 50K diamond and
then use my normal oxide. If the epoxy doesn't look good at that
point, I use ZAM to finish things off. Just keep in mind, the epoxy
will probably undercut slightly no matter what you do.
Cheers from Don at The Charles Belle Studio in SOFL where simple
elegance IS fine jewelry! @coralnut2