I go into my game now and all of a sudden the Minor Faction Potential, and the AI options that were there in 6.2 are now gone in 6.2.1 anyone else have this happen to them?

Just checked: Still there for me. 

AFAIK you can not en-/disable these once you have started a campaign, but only before a new campaign.

They moved the ui

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CA-Pingu#2295 wrote:

UI

• Moved "Minor Faction Potential" and "AI Strength & Threat Assessment" checkboxes from endgame settings to general campaign settings (this will not affect current campaigns).

With the hotfix from this week.

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ah i guess i didnt check the menu fully, i was looking for it in the normal place, thanks you letting me know. i thought something was wrong with my game.

nope just started a new campaign tonight, the options still arent there, they are nowhere in any of the campaign options, general, battle, advisor, nowhere

Check here

Are you using Immortal Empires Expanded? Not sure if it has been fixed but last time I played it was not implemented yet there.