tl;dr: My commander got stuck orbiting the inside of the star after trying to use an orbital transport to flee the moon I threw at my enemy. Basically, I got driven off the start planet to a moon in a different orbit. In a fit of kamikazi fury I decided to throw my escape moon at him, and get my commander to the moon orbiting the start planet. I think I was in orbit around the star when my moon actually hit, and after that my commander and orbital transport were stuck inside the star, orbiting rapidly, the path terminated completely. Oh, the moon missed his commander too, so I just lost out on everything there
common, but your commander, and any units orbiting the planet that you have sent elesewhere should have continued to their destination from the sun. if not, i am clueless.
I think its cause I was still technically in orbit around the moon that died, I dunno, the timeframe is a little sketchy (and it happened 2 days ago)