zs code:
mods.enderio.AlloySmelter.removeRecipe(<enderio:item_alloy_ingot:1>);(which is energetic alloy)
Recipe still existed, with no error in the log.
But adding new recipes succeeded.

EnderIO version: 5.3.70, EnderTweaker version: 1.2.2.

Well, it seems that there is no such problem in Version 1.2.1

I can confirm what @VillagerGold said. I was using

• EnderIO version: 5.3.70
• EnderTweaker version: 1.2.3

and was having the same issues as @lunareclipse-64. Recipes could not be removed, but recipes could be added. I tried changing my EnderTweaker version to 1.2.1, but got a crash resulting from an invalid reference to code in EnderIO that didn't exist. So I changed my EnderIO version to 5.2.66 (to match the dates as close as possible). Now everything works precisely as you would want, even on the most recent forge version: 14.23.5.2859. So, as long as nothing in forge changes to make this version of EnderIO and EnderTweaker break, everything should be fine. You just miss out on any additions to EnderIO since that version (nothing vital).

Summary
This doesn't let you remove recipes:

• EnderIO version: 5.3.70
• EnderTweaker version: 1.2.3

This results in a crash:

• EnderIO version: 5.3.70
• EnderTweaker version: 1.2.1

This lets you remove recipes:

• EnderIO version: 5.2.66
• EnderTweaker version: 1.2.1

Hopefully that is enough information to discern the problem (which is probably a change EnderIO's code that EnderTweaker never accounted for in its updates passed 1.2.1).