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Then the persistent was not important, or even needed in the first place.
Every mod, icpatch, whatever will bork your game/saves and even the persistent. That's a undeniable fact, peroid.
A savegame, created with installed mod A can only be used in the next update with the installed mod A, it will not work with mod B or on a clean installation like intended from the dev.
So stop blame the dev for your messing with the game files.
Its the same, if you have a Stellaris game session that is modded to hell and back and you move to the official paradox help forums to complain why the super rare xyz quest refuses to get triggered.
Take your complains to the modder, the dev provides you with a game that works if it is played as the dev intended - namely with a clean unmodded installation.