This can happen unfortunately. One thing to try is to start WMR before you start MSFS. I find when I do this that I can sometimes switch out of VR and back into it later, although the 2D performance in between that is usually terrible and that can be fixed by closing and reopening WMR.
The only way foolproof way I have found to get around it is to simply avoid reentering VR. To do this, start your flight in 2D and only when you are ready to go switch to VR and leave it that way. I actually start my VR session while on the world map and prep my flight and fly it all in VR as it is much more immersive that way but I understand that it is easier to prep in 2D.