I'm not surprised really
I've added units etc dozens of times during a game
I usually just start a game and continue it when I have made changes to a mod.. usually works (and with usually I mean I can't remember it not working, except sometimes the mod doesn't seem to have updated but then it will later, new sprites work too.)
I still wonder about changing a magic site in an indie province (on start of game at least) which was not your capitol into a capitol site (nation specific) since I never tried that.
__________________
Want a blend of
fantasy and
sci-fi? Try the total conversion
Dominions 3000 mod with a new and fully modded solar system map.
Dragons wanted? Try the
Dragons, Magic Incarnate nation.
New and different undead nation? Try
Souls of Shiar. Including new powerfull holy magic.
In for a whole new sort of game? Then try my scenario map
Gang Wars.