you can just update millenaire whenever you want, as long as the savegames you care about don't get loaded when it isn't, the villages will stay active, if you do, the savedgame is fucked.
your backup probably will do though.
K wait. What the hell am I supposed to do to make the village active again once I put the backup in?
Edited:
I cannot play this mod knowing that every time there is any sort of update it breaks and my villagers are taken away from me forever. Its a pitty too, this mod is awesome. Oh well back to terraria considering notch continues to break mods.