Firstly, thank you for great modpack!
Secondly, I found issue with many (regular crafting) recipes and cause of it.
While editing recipes via CraftTweaker, to remove recipes you use recipes.remove(...) function.
Method recipes.remove(...) attempts to remove all regular crafting recipes.
In cases, when item has both shaped and shapeless (marked with crossed arrows in JEI) recipes, this method makes impossible to craft certain (sub-)items (based on damage and especially, on NBT).
Items I found affected by this issue:

• All charms from Cyclic (unable to repair ones due to removed shapeless recipe);
• All dense and vacuum versions of opaque ducts from ThermalDynamics.

I'm sure, there are other items affected by this issue (but I didn't find ones yet).

Solution:
Use methods recipes.removeShaped(...) and recipes.removeShapeless(...) respectively instead of recipes.remove(...) to avoid such problems. And beware of use of recipes.remove(...) in cases, when item has both shaped and shapeless recipes.

Modpack versions: 1.45 - 1.46

I am aware of how recipe removal works, the use of recipes.remove is intentional.