I've found the savegames to be pretty tampering-resilient if you dont change entire tech positions and the like and just edit names, values and such of existing elements. BUT I believe there should be a models.csv in the mod config folder, so something is amiss with your game. I think the fix itself is as simple as giving the new elite units different id's. That or giving all the nations a proper ship class name for every class of corvette/frigate/DDG. But I'd be happy if someone more versed in modding could deny or verify this.
Edit: the elite units are in the mods.csv
Editedit: The elite units have the correct id's, that are different from nwo's units, in the division_types.txt. I tried editing the models in mods.csv to correspond with those id's (50-somethings instead of the 40-somethings nwo ships use) but I guess I missed something since my game wont launch anymore.