In case it is still of use and not already solved in 1. 9. While rummaging around a bit in my aurora manual backup folder, recycle and backup bins in an unsuccessful search for a buried replica of the 1. 8 Antarctic db described in my earlier post, I found that the new, less setup-intensive game I started after that, shows the same issue caught at exactly the right moment, and this time, without any obvious Microsoft in the head disturbance to Aurora saving or loading. In the db, ground unit formations seem to be there: names, IDs, parent formations, locations and all; and the formation elements, too, as far as I can tell; but from this db, none of them load into Aurora, and with any subsequent save (including load/do nothing/save/quit), the units vanish completely from the records. – At least the player units, I don't know about NPRs.
One thing I notice in the db is that some NPR formations seem to have both PopulationID and ShipID set to 0. I don't know what that means and if that's intended, but it feels like an error. Maybe some bugged NPR unit transport? Or a save issue after all? Or it may be a different disappearing units bug from the main one as someone suggested.