Fine. I then made a new Skyrim install, placed Eola into it... And eventually, when I got to the end of Dragon Rising, there was lydia... My modified lydia. Her .esp was not in this game, but there she was. All I can assume is that copying the stacks of spells and perks somehow also copied her other characteristics, ALL of them, and tacked them onto eola, such that they invisibly tagged along until lydia showed up.
If anyone can explain this, or better yet tell me what I did wrong I'll be eternally grateful. (Well, not eternally, but you get the drift...)
If no one can explain this, then I guess I was the lucky person to find a 'gotcha'.
