There's a glitch where TFC pickaxes aren't harvesting end stone. They can destroy it, but it won't drop as an item. It does drop as an item when using MC pickaxes.

Edit: this also applies to bedrock when using mods that allow the breaking of bedrock. This glitch didn't exist in some of the previous 1.12.2 alpha .jars.

Resolved in the latest version, 0.2.0.34!

I'm dumb; I forgot to remove "drop": "minecraft:end_stone", from a certain config file (which forces it to drop even if it won't under vanilla circumstances) before testing. I removed that line, tested it again, and the glitch still exists.