If you uninstall mods to check something, or upload a save file, it shouldn't overwrite ALL your custom factions to an unmodded state and then save them that way so that when you turn the mods back on all your factions are broken. There should be a way to either tell the game NOT to update the factions, or to roll back the updates when you re-enable the mods.
This is especially bad considering the game has profiles for mods, implying that you're supposed to be able to swap profiles, but doing so just permanently breaks everything using those mods, who then all have to be manually fixed once you switch back.