When you add or remove any mod (not this one) it resets all the player stats back to 0, which means you need to reset the skillpoints and reassign them.

Even updating a mod breaks it

Just tested here and it does NOT happen on my side. Must be something else...

Same thing happened to me. I disabled the extended vanilla mods because the inventory items were not usable in the extended vanilla extra armors. Specifically, I couldn't add robo ports. After I disabled it, all of my stat buffs are not applied. They still appear when you look at the RPG System screen that lists your level and stats, but they are not being applied.

EDIT: in case anyone else runs into this, the console command /rpg-reset-points will reset all of your stat points and you can just re-apply them. Thanks for the "in case of emergency" option MFerrari! I'm back in business!