I conquered some FEs [War in Heaven] and had a similar problem. Seeing as I already ruined my ironman playthrough by needing to save-game-edit because of a corrupt species causing a crash I decided to just destroy the old capital in the GUI, go to the console, and run effect set_building building_system_capital ... That would spawn a "colonization" capital on the first of the next month which was "good enough" for me.
Note: I wanted to play all the way through but there's too much micro to "own the galaxy" for me even playing on a Small Galaxy. After the contingency spawns and is then put down I'll just make a new game with habitability 0.25 and see how that works out.