The problem as I see it is there are events that exist which just give you +influence with no loyalty to go with it and no second options. You're forced to eat that influence hit and ruin the perfect balancing you had to do to get it where you wanted it to be.
Every estate has one of these events that add 10 or less likely 20 influence (determined before you click the button so the tooltip will tell you how much). They can't retrigger until the effect from the event wears off. There is also a companion event that reduces influence without you doing anything that follows the same rules.
If you conquer land you indeed keep the landed powerholders in that land unless they're from another religion. As a Christian you won't have to unland Ulema in conquered lands but you will have to honor the agreements other rulers made with the Church or face the consequences.
To take another example Burghers in Riga will be upset if you revoke the city privileges for Burghers in newly conquered Danzig, even if those privileges were not granted by you personally.
I will forward your concern that the game does not warn you about this on conquest though (in the meanwhile it is fully visible in their province windows and you likely do want to look at those anyway when selecting provinces to see which ones you want).
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