Once you meet up with an npc who can join the party, their base proto (used thereafter as an underlying reference for their current level) gets placed into your save-game data for the remainder of the current game. Even if you go into the save-game files themselves and delete the proto, gameplay with that particular npc will still be screwed for the remainder of the current game. Unfortunately, the only way to get out of a mess like that is to: 1) delete the npc's base critter proto from your data directory (if you modded the base proto, put it into master.dat instead), and then 2) forget about saved games and start playing over.