Happened to me as well. Everything (not just the .CFG file) in the FSX folder (C:\Users\Name\AppData\Roaming/FSX) was result to default, and all of my backup .CFG files were gone, as well as the modified dll.mxl file and it's backup(s).
When I stared looking around I noticed in the same location a newly created folder named "FSX - App Data Folder" and lo-and-behold in that folder was my correct .CFG and .XML files with all of the backups. I made backups of both and re-named the "FSX - App Data Folder" to just "FSX" and Flight Sim launched normally with all settings intact.
I launched and played FSX a bit Friday morning, and everything was normal. Then today the strange folder thing happened.
The only thing that changed was, when I shut down on Friday, Windows went through an updated that finished when I booted up again.
I'm running FSX SE in Windows 7.