I presume by “hot changeover,” you mean you land and taxi to parking, then load a new flight plan to head back out on another trip without returning to the main menu? I haven’t done back to back trips, but have you checked for any discontinuities in your flight plan legs after entering the new flight? I also made a video about the new AAU update for the CJ4 a while back that may provide some clues as well. It’s kinda long but I have chapters marked to make it easy to find the flight planning sections.
There’s also a dedicated CJ4 support thread you could look over (which this may get moved to anyway).
I fly this almost exclusively, but sorry I can’t help more directly. I may try to recreate your scenario later today/tonight and see what I find.