Well I wanted to remove the Silicon recipe that the Manufactory has, but it doesn't work and gives me: No such member:nuclearcraft

Could you paste the line of script you're trying to use?

mods.nuclearcraft.manufactory.removeRecipe(appliedenergistics2:material:5);

Hmmm - don't know the answer to that one - I'll look into it.

I have the same problem and while checking something else with CraftTweaker I did a /ct dumpzs and NuclearCraft wasn't listed under Root/mods.

Here is my CraftTweaker's Registered Modlist:
https://i.imgur.com/WG7PUFC.png

I hope this helps.

Fantastic - thanks to this commit, the issue should be gone :)