Logging into Horizons will put you in your ship. Just tried Inter Astra and transfer worked - shows the ship is on its way
It works most of the time. The steps I took to get into that situation were:
1) Left my ship and shuttled to another system
2) Died on foot with a bounty
3) Respawned at the prison ship, in my ship, that I'd previously left behind
4) Jumped out, got a Black Adder error
5) Respawned at the prison ship on foot
6) Summoned the ship back to the prison ship, shuttled back out
7) Tried to summon my ship to the place I arrived at, couldn't. Uh-oh
E: AHA. I just docked at another station, disembarked, and couldn't go back to my bay because my ship was impounded. I think that might be the problem - at some point in all those prison ship shenanigans, an impound fee was placed on the ship, but the game didn't present the UI for paying it.