After more testing, it does the same thing even if I create a direct VFR flight plan from airport to airport. I have not tested with IFR yet but it seems to be with a plan that’s already loaded, not just LNM plans.
I did have once where it actually reset the plan before it and loaded the second plan just fine. This happened after I loaded a flight plan and it was reset to just the departure and arrival airports after trying to select a runway. So I loaded up another flight plan and no crash.