I am having the same trouble. I landed at Black Rock and left the plane there while I had dinner. I came back and took off then noticed that the nav LOG was not working. I continued the flights using SkyVector maps and made it to Susanville three times. Each time it tell me that I complete the flight, but when I return to fly again It starts at Spaulding (1Q2).
I was think I’d delete MSFS2020, but can’t fine the file to start over. Maybe you could write out the steps that I could try and follow. I’m sure from what I’m reading there are a lot of people in the same plane!