Strange traits bug

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I recently decided to try to install the Alexander EB minimod to my comp, but I noticed it really screwed up my characters' traits (changing their races, making them all client rulers, giving them other factions' victory conditions, etc.). I had made backups of the save game files prior to attempting this installation, so I did a complete reinstall of EB and copied the backup save files into the right directory. They're a lot closer to what they were before now (e.g. my Molossos characters have changed to Chaons instead of becoming Sogdianos), but a lot of the traits are still wrong, such as Pereginesis traits for regions I haven't conquered, all my FMs having the 'client ruler' trait, and the race issue. Is there any hope of restoring my game, or is it as good as lost now?

EDIT: I also just noticed that the minimap shows me (Epeiros) as controlling Numidia and Carthage as owning Crete, when it's the other way around.