First you have to be aware that the flight load/save/auto-save functionality provided by FSUIPC completely rely on the functions provided by the MSFS SDK, namely the SimConnect functions SimConnect_FlightLoad and SimConnect_FlightSave (as well as SimConnect_FlightPlanLoad). Although the SimConnect_FlightLoad function is documented as working, the SimConnect_FlightSave function (as well as the SimConnect_FlightPlanLoad function) is still documented as 'NOTE: The current status of this function is NO ERROR, NO RESPONSE.', which is Asobo's way of saying that this function is still not 100% working/reliable, It has been this way since release.
Therefore the saving and loading of flights is still not 100% reliable, although some users have reported more success with this than others (maybe aircraft dependent). If it is not working, I cannot do much about this - you can try raising a bug request with Asobo, but they may reject this if the flight file is generated by the SimConnect_FlightSave function as they are already aware of issues with this.
Flight files generated by MSFS2020 itself and those generated by external apps (using SimConnect_FlightSave) should be compatible/the same, but this may not actually be the case at the moment. You could try loading the flight file via FSUIPC7 (File -> Load Flight) to see if that makes a difference. You can do this either when in the World Map, or when you already have an aircraft loaded and ready-to-fly.
John