Like I said, even if you do need to use it sometime, just make sure to save right afterwards, and then exit the game completely.
The worst thing that could happen using mods is as Kevin mention OR getting the achievement inmedately, due to the mod automatically meeting the achievements criteria, such as giving you X item or unlocking X tech or whatever achievements are there. Modding is now officially supported in Afterbirth+, enabling users to mod the game using the Lua programming language and to upload their creations to the Steam Workshop.
