Most of these capacitors don't even work in an Anti-barrel and it gets dangerous to have too much NBT data stored in one area. Keeping all of the loot capacitors that came out of my mob farm/lootbags corrupted a chunk of mine. I'd like to put them through a crafter or something that can strip the NBT data and stack them without losing all of the benefits entirely.

But the nbt data is how they are useable in machines. If you remove that they will be no longer usable in machines.

Could we make a machine that eats loot capacitors and spits out weaker generics? This would be a better solution than trashing all loot capacitors which is currently the only thing I can do to prevent chunk corruption from storing massive amounts of them.

You could make a shapeless recipe using CraftTweaker and then use the EIO Crafter or another auto crafting system.

Yeah that's the best option. They really shouldn't be able to cause chunk corruption by themselves, unless you are storing thousands of them. It doesn't really make sense to add a mechanic to make them more generic since really, you can jue take a regular capacitor then.