I confederated Alarielle but she stopped providing her bonuses to regions anymore. Before the confederation, I was able to see the mark and bonuses she left on regions where she ends her turn. After 5 turns of the confederation, she still can't do that.
Apparently, loading a save immediately after something happens on legendary difficulty breaks the game. I quit the game on the turn I did the confederation. After I came back to play, I noticed the bug. In another campaign when I was playing Lizardmen, I saved and loaded the game right after I got Lord Kroak. His equipment items were all gone (empty equipment slots) after the load.
I can not try and reproduce the bug because I'm playing on legendary difficulty. Confederating her was also a miracle. It would be hard for me to test again.