Clear casting drives me crazy! Clear resin is tricky to cast and even trickier to fill.
I have successfully filled resin with resin, but there's a challenging balancing act. If you rough up the inside of the bubble so the filling resin has some tooth, you often get a foggy outline of the hole visible in your finished clear part. So I would only recommend scratching up the surface if you were using opaque resin.
On there other hand; if you leave the inside of the bubble smooth, the interface between the casting and the filling resin should be less visible, but I have had the filled bits pop out because they don't bond as well to the smooth surface. This typically happens when the bubble is a open bowl shape, as opposed to a hole that has a slight undercut - (those stay trapped, but are harder to fill).
Either way, when light shines through the clear resin at the right angle, the filled bubbles can sometimes be seen. That may be just fine if you are creating a"natural" crystal look. If you are after perfection, I would recommend doing a fresh casting with a slow setting resin and vacuum degassing it after mixing, and then pressure potting it while it cures in the mold.
I hope this helps. I always hate telling people "you need to buy a bunch of fancy gear to do that right". But clear stuff is hard.