In general terms I would not try to redrill a bead to enlarge the perforation. This causes breakage—particularly in crystalline minerals, like amethyst. Agate can be tougher.

But my approach, when it is needed, is to abrade the perforation. I use a jewlery saw mounted with very fine blades, or with abrasive line. It is arduous work. But if you have to do it, it is possible.

Jamey