Steps to reproduce:
LootTables.getTable("minecraft:chests/abandoned_mineshaft").getPool("Ender IO").removeEntry("item_basic_capacitor18"); doesn't work

LootTweaker: LootTweaker-1.12.2-0.0.7
CraftTweaker/Minetweaker: CraftTweaker2-1.12-4.1.9 / modtweaker-4.0.13 / MTLib-3.0.5
Forge: 14.23.4.2759
Minecraft: 1.12.2

EnderCore-1.12.2-0.5.37
EnderIO-base-1.12.2-5.0.31
EnderIO-conduits-1.12.2-5.0.31

Logs, scripts and other useful information:
Using setRolls(0, 0) on the EnderIO pool(edited) did work in disabling the whole pool though

Just FYI, as of Ender IO 5.0.33 we switched to using this method of adding loot: https://mcforge.readthedocs.io/en/latest/items/loot_tables/#adding-dungeon-loot

@HenryLoenwind That's the way LootTweaker expects it to be done, so all should be fine. What did you have before? I distinctly remembered making a PR to EnderIO (which was merged) to make it use the loot table system correctly.

Before we used the "code" method, the code is still there: https://github.com/SleepyTrousers/EnderIO/blob/master/enderio-base/src/main/java/crazypants/enderio/base/loot/LootManager.java#L95 (I use it together with loottweaker to create the content for our json files )

I've finally got around to looking into this. Ender IO's post 5.0.33 code is fine. However I need to provide a way to edit inject tables, such as the ones Ender IO uses. This is going to take some thinking, as inject tables are not registered, and I don't think they should be.

I wonder if it wouldn't make more sense to add a folder in 'config' that has highest prio in loading loot table assets. Dump all tables there so people can just edit them...

@HenryLoenwind
That defeats the point of LootTweaker, which is modifying loot via ZenScript instead of JSON.

Solved by 6e1bae8. A release will be coming once I finish the documentation.