I wonder whether you have the Heis of Alexander pack?Sorry for the double post, but I think there is something weird going on.
I deactivated all my mods when I did the last test and I could see (and delete) the Fortresses.
I remodded it carefully and started playing, noticed that the Francia mission vanishes when you start it and a day passes.
Deactivated all mods again , tested that part again and it still vanishes completly after a day.
I then reactivated some mods and started playing, planning to finish all tasks at once when I can do so.
But then, after I won a hairy war, I noticed that I could not delete fortresses again.
I removed all mods and even all saves - but this time the Fortresses stayed invisible.
I have honestly no idea what keeps going wrong.
Sorry for the trouble, I am just really looking forward to playing as francia.. x_x
Is it possible, as a hotfix for my current game, to remove the buildings via save editing?
Given that you have issues with the unmodded variant, too, I'd suggest repairing or reinstalling Imperator.
Editing is a possibility but it's certainly quite tedious.