Unchecking/Checking MIGHT be needed only if Fenix updates the stock model exterior of the airplane. I said MIGHT, because the way we patch the liveries is done following Fenix suggestion, so the installed liveries shouldn't be affected by updates of the main model, at least in most cases.
Instead, just ENTERING the GSX Config Page, let it reload the list of airplanes and exit again IS 100% required and mandatory ( and explained in the manual ), if you add a new livery after the last time you ever entered the GSX Config Page. Failing to do so will GUARANTEE you will have Passengers disappearing as soon they sit.
MSFS 2024 adds an extra problem: due to its extremely restrictive LOD, it's possible everything has been configured correctly, but you'll still see passengers disappearing. This case can be confirmed if you notice all already seated passengers will appear again if you move the Showcase/Drone camera closer to the airplane and close to its center of mass. A possible fix in this case would be disabling the Dynamic FPS feature in the sim, and be sure the Object LOD is set at 200.