I just had a geo-survey finish construction. I had auto-assign on, and it assigned a free officer. I didn't like that officer for the job, so I assigned a different officer (my fleet survey officer). I'm 99% Aurora did NOT pop up a "do you want to replace the existing commander" box. At this moment both officers think they're the commander of the ship - in other words the old officer did not get bumped. The ship thinks that the old officer is its commander. The fleet survey officer slot is empty, i.e. the new officer has left his old billet.
I think they're going to grab a pair of cutlasses and have at it on the bridge to determine who gets to run the ship
This was actually my 2nd survey ship that I built, and almost-identical scenario played out the first time too (with the same "old" commander - I'm trying to drive him into a deep depression). I think (but am not sure) the only difference is that I did a 5-day timestep before trying to replace him. Everything seemed ok the first time this happened.
[A few minutes later]
OK - I just assigned the old officer to the fleet survey post. After I got him out of the way, the ship (and it appears everything else) decided that the new commander was in charge after all, even though I didn't do anything else with him. I'm probably going to relieve and assign him again in hopes of cleaning up any remaining corruption in the database.
John