Same issues here; OneDrive deleting files and folders. Fortunately, the deleted items appear to be in the Recycle Bin, but haven't checked this rigorously. I use Onedrive across a couple Win10 PCs, and a iPhone and iPad, and I'm betting the issue is something to do with cross platform synchronization where the local files on some devices can be quite old, and OneDrive somehow cannot resolve which versions of the folders and files are the newest. I have received the message (in the past), mentioned in prior emails in this string, of the mass deletion of files, but of today's file and folder deletions, I received no notice, which is disturbing and also requires Microsoft's investigation.
This anomaly is embarrassing and does require a fix.