Interestingly, when I killed all but Jas and Luki in Cook's save, all but the commander slots emptied, so it's strange that it didn't do that for you.
What command are you using to remove nobles from positions?
gui/gm-editor
I am explicitly delving through the data structure rather than using any commands, the necessary functions to fix many of these issues simply do not exist as DF-hack scripts.
Still working on the investigation, things are progressing interestingly. There seem to be currently two types of crashes I can experience. The first is that if I'm on the timeskipping calendar screen, such as when you start adventure mode or fort mode without a current game in progress, if the date reaches the 6-7th of Hematite, the game will crash. Even at a later year. So every year, something happens about at the start of summer that will crash the game, but ONLY when the game is not currently in progress, as this crash does not occur during fortress mode. Human caravans do arrive at about that date, so that might have relevance,
Secondly, both in fort mode and during the timeskip screen, at the very end of the year, the game will freeze/crash.
These could be related, but also could be separate. Currently I'm testing every single year from 929 (current) to 1000 to see if there is a moment in time where the crashes end. I will hopefully use that information to find a solution from there, or, if the crash subsides at a resonable time, perhaps recommend we move forward to it. I've got plenty of day left, so I will do my best to right the save.
Another interesting finding in time passage. When only Jas is left as an active unit in Silverthrone, any amount of time can pass without crashes, leading me to once again believe there is a corrupt unit or units in the site. This may be related, as NGN suggests to the many traveling units in the site. During my turn I made liberal use of the squad off-map raiding mechanic to grab all the books in the surrounding abandoned monasteries, I did not realize at the time how buggy that feature was. The testing continues.