They didn't convert on the latest beta patch (2.2.4), which I'm playing on. I'm pretty sure it worked as intended in 2.2 and the earlier patches, though.Shame about the forts -- the Aegis Complex generates a ton of amenities in addition to the enforcers. I don't know if those are included in the patch or not; I suppose they'll probably convert to standard buildings too. Can't test it since I've already annexed all the FE worlds in my current game.
I'll take this opportunity to advertise my very own fix for the hive building. A mod that adds a decision to check which capital building is appropriate, and convert it accordingly.Had the same issue. At least on the FE world I was able to destroy the capital building, after which it was automatically replaced with a ship shelter that I could then upgrade. I was unable to do that with the hive building, however.
*edit* Also, replace their FE 'fort' with either your own fort or a precinct.