I select the minor settlement i want to merge into the bigger one - click on zone merge orders. Popup - opens. I set the checkmark to where i want the zone to merge into. The info says 100% will rebel, so i click on ABORT. Zones merge and population moves.
I did this again with another zone that said 100% will rebel to test and it merged aswell.
Then i went to a third zone that said only 29% will rebel. I set the checkmark and clicked on ABORT again ... it still executed the command (like in the last two examples) but this time failed with all the negative modifiers.
I can provide a savegame i suppose if needed. But this isn't expected behavior when clicking on abort