Yes, it sounds like either windows deleted MW's user files, or a disk cleanup program is doing this, and upon restart, MW re-created the missing folder/s with new factory ones.
Unless you had a backup you'll need to manually set MWPro up how you like sorry.... OR, you could use windows system restore if you wish, details here:
https://support.microsoft.com/en-us/win ... 6777ecd14e
Note you can backup via File>>Export in MWPro once you have it back to how you like.
Any problems, please let me know.