Theres a program called Any Game Starter. It basically creates different environments for your save files, so you can run a mod-free file while using mods in another one. I think it also allows you to select which EPs you want to play with in each save file.
I downloaded it from Mod The Sims. I downloaded it yesterday though and I'm still figuring out how to use it exactly so hopefully someone will tell us here, or recommend another program
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EDIT: I just noticed you already knew about the factory reset thing so I deleted that part of the message
. Too many things in my head, sorry.