It is possible for the state saving to get confused between updates, especially after large product updates which have a lot of changes, as the aircraft may be attempting to load a state that was only possible in a previous version of the product. One thing I'd recommend trying is deleting the StateSave.ini file from the relevant file directory, and it'll then regenerate the next time a flight is loaded with the RJ with the correct state saving options available.
MSFS 2020 - MS Store:
C:\UsersUSERNAME\AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe
LocalState\packages\justflight-aircraft-rj\work\PanelSave
MSFS 2020 - Steam:
C:\UsersUSERNAME\AppData\Roaming\Microsoft Flight Simulator\Packages\justflight-aircraft-rj
work\PanelSave
MSFS 2024 - MS Store:
C:\Users\USERNAME\AppData\Local\Packages\Microsoft.Limitless_8wekyb3d8bbwe\LocalState\WASM\MSFS2024\justflight-aircraft-rj\work\PanelSave
MSFS 2024 - Steam:
C:\UsersUSERNAME\AppData\Roaming\Microsoft Flight Simulator 2024\WASM\MSFS2024\justflightaircraft-rj\work\PanelSave
Hopefully, that should resolve any issues you may be having with state saving.
If you continue to experience any of the behaviour you have listed, could I kindly ask you to raise a ticket with Just Flight Support via the following link: https://www.justflight.com/support
In the ticket, if you are able to provide any screenshots/videos that are relevant to what you are experiencing, as well as any steps on how the behaviour can be reproduced, then our support team will be in the best position to be able to further assist with this.
Mark - Just Flight