MC: 1.12.2
Forge: 65 and also tested 68
TR: 824
Rcore: 335
CraftTweaker: 1.10

Script used: recipes.remove(<techreborn:lapotroncrystal>);

Got: cloaking device, chainsaws, drills e.t.c recipes removed

This sounds like this one CraftTweaker/CraftTweaker#627 . Update your version to 4.1.11 and look if it till occur.

Otherwise you should try to use recipes.removeByRecipeName("RECIPENAMEHERE"); to solve this issue. You can see the name by clicking on an output in JEI. It is called recipe ID.

yep, doesnt seem like something I can do anything about which is why I was wondering what was up