I kind of had the same problem with the Steam version after upgrading my Mobo and CPU, but kept my old M.2 SDD with MSFS already on it.
In my case, the files and folders inside the “official” folder inside my game install directory were all gone. That seems to have been because I also reinstalled Windows, and the new Windows had no ownership of the files, so did not display them.
What I did was to boot the system from my old Windows installation, and made a backup copy of the whole “offical” folder, and then took ownership of the folder via the “properties → security” pane when right clicking the “official” folder. Thereafter, booting from my new Windows installation, the files were all there, and MSFS did start.