If I wanted to edit/replace a crafting recipe or item that already exists in the game, would I be able to overwrite them using a mod folder or would I have to replace game files?
Well if you're okay with the original crafting recipe still being there you can do it with a mod folder mod. But that could get clunky (if you know, your recipe refines ore into 3 ingots at higher levels, you end up with two refinement recipes that look exactly the same aaaand yeah.)