Ok, I think I know what happened with Connie:
RotC’s leader system was designed around making Companions leaders. Normally, Companions don’t start the game attached to a settlement workbench. Connie Abernathy, who is not a Companion, starts the game assigned as a settler to the workbench at Abernathy Farm. By using one of the add-on mods that allow NPCs who aren’t companions to serve as leaders, you were able to assign her as a city leader (I use two myself).
So far, so good, right? I assume Connie was physically in Abernathy Farm, probably picking tatos and arguing with Lucy. When you assigned her to lead at Red Rocket, RotC told her to physically move to Red Rocket and take over. It probably did this by telling her to, from now on, stay within a certain distance of the assigned City Planner's Desk.
However, for whatever reason, RotC did not reassign her as a settler to the workbench at Red Rocket. She was likely still a settler assigned to the workbench at Abernathy Farm. Because of that, when you opened the Red Rocket workbench, it didn’t see her as a valid settler, so it couldn’t reassign her.
By creating a City Planner’s Desk at Abernathy Farm and assigning her as the leader there (nice call, woodfuzzy!), RotC once again told her to physically move to Abernathy Farm, take over, and stay near that City Planner's Desk. Since she never stopped being a settler assigned to the workbench at Abernathy Farm, all is now good.
Hope that makes sense.