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I have also noticed this. All family prestige seems to be reset upon reload for all families in my country. Playing as Macedonia that leaves me with three families with 1000 prestige and the rest have none and will never get any. I have on several occasions checked the family prestige during gameplay and it does move, so that's not the problem. This is not a major thing when you play a monarchy, but I imagine it could be if you play a republic.