Actually, this problem has happened to my work laptop 4 times since July 31. The most recent deletions was twice today. Each time it creates a new profile, 000, 0001,0002, etc. It leaves the folder structure intact, but deletes the contents of all the folders.
My stuff was actually safe in the previous folder but before I had time to copy my things, a couple of hours later, it created yet another profile. This time, everything went - contents of desktop, docs, photos, videos. and all preferences, but folder structure is still there.
My stuff is always backed up to a portable drive and I only leave stuff on my desktop that I can afford to lose, but I'm getting tired of re-syncing my bookmarks and other customizations such as wall papers and power schemes.
For the record, I'm on 1809 Microsoft Windows [Version 10.0.17134.376] Surface Book.
Frankly, I'm the only one in my organization with the problem (that I know of) so tomorrow, I'm just going to image it and start over and hope a fresh copy of Windows will make the problem go away.
Just to add to my comment above, this all happened in the middle of trying to uninstall Office 365 Pro Plus to fix sync problems with OneDrive. I was stuck with a conflict between OneDrive and OneDrive for Business that I never did resolve and was attempting to reinstall O365 as a fix. Upon reboot, I was treated to another new desktop and no folder contents.