By default OneDrive comes configured to backup the entire user folder, it overrides the default user structure. It creates a labyrinth of shortcuts. This messes with other applications that expect a default user folder hierarchy, but sometimes it fails to resolve the correct links. You effectively end up with two user folders that coexist on the same symbolic links and are both present in your computer at the same time (different place on the harddrive but same place for the OS). This wouldn't be a problem if OneDrive were only backing up the folders one way. Unfortunately, it is actually syncing the OneDrive and your folders bidirectionally, and this includes deleting files and folders.

Thus, if another program or another computer associated with your active directory user account messes with the folders at the same time, there exists the possibility that OneDrive confuses your empty user folder, with the virtual user folder. It believes the empty folder structure is the newest and most updated version. Because internally it only has time stamps but it doesn't store metadata on the procedures. It sees, file existed at 01:33:12 and no longer exists at 01:33:13, it doesn't know why it doesn't exist anymore. Now it thinks this computer is outdated and it proceeds to sync, erasing all files without prompt.

I've seen this happen at least three times.