So, I was playing the Terran Alliance. Built some small and medium-sized ships (the Marklar Mk1 and the Marky-Mark Mk1, respectively). Upon load, all of my Marky-Mark ships disappeared. Just weren't part of the fleet any more.
First time it happened I thought maybe I had accidentally obsoleted them and decommissioned them. So I then upgraded the ship... Put some better beam weapons on it. Played the game for a while. But then on loading the next day, the Marky-mark Mk2s all disappeared.
Not sure what's special about the ship. There's a rotating circle component on it. There's a reinforced hull point. Some plasma weapons and armor.