So I was playing a game with my brother the other day, and for whatever reason he kept his flagship with his fleet as we rolled over the map. At one point he jumped into an advent gravity well with his titan, flagship, dozen or so capital ships, and assorted frigs/cruisers. He sees they've got a fleet, starbase, defenses etc prepped so he decides not to fight and jumps back out. The advent had researched the ability that lets you capture 5% I believe of retreating ships. So as his ships jump out, the Advent player manages to capture a couple. Don't ask me how, but he captured my brother's flagship. He didn't listen to me shouting turn off auto attack and press stop for his entire fleet, and thus did his entire fleet turn on his flagship and promptly remove himself from the game. We still haven't stopped laughing with (at) him for this, but I cannot help but wonder if that is supposed to be possible. I would assume not, as it seems overpowered. Naturally he shouldn't have had his flagship with the main combat fleet anyways, but it still seems like it shouldn't work
tl;dr flagships are capturable by the Advent (Loyalist I think) Research where hostile ships leaving your gravity well have a chance of being captured