OneDrive automatically deleting files from OneDrive folder

Likely Solution:

Hey there, I know this is an old thread, but still a current problem.  Please check and see if you have any folders synced in your OneDrive agent from SharePoint that is a child or nested folder of another folder synced by your OneDrive agent from SharePoint.  The reason this happens is that your have synced a parent folder and child folder.  Lets assume you have two synced folders in your OneDrive agent.  FOLDERA and FOLDERB where FOLDERB is a nested folder within FOLDERA on SharePoint (for example DOCUMENTS\FOLDERA\FOLDERB.) In File Explorer your OneDrive agent displayes the following folders: 

YOUR ORGANIZATION SHAREPOINT (The little office building icon)

   SITE - FOLDERA

               >FOLDERB

   SITE - FOLDERB  

When you drag a file in FOLDERB via File Explorer, it gets uploaded to SharePoint under FOLDERA\FOLDERB\NewFile.txt.   FOLDERA from you computer then syncs and does not have the file present and deletes it from SharePoint, then updates FIOLDERB and appears to delete the new file immediately.  

Try to remove one of the synced folders (The parent or the child) and try again to see if the uploaded file now persists.

I don't think that shutting down had anything to do with it.  When it happened to me multiple times, I had not shut down or restarted or anything out of the daily ordinary stuff.

This just happened here, but a notice popped up and an email arrived a few minutes later warning a large number of files had been sent to recycle bin at 9:09pm

I was nowhere near them so how on earth did that happen.

They seem to have restored OK.

I did notice some kind on internet slow down so had rebooted router about then, could that have caused it if it was trying to check sync just as I shut it down?

That really ought not to happen surely but a clue as to what's going on.

Over two years later since this thread was created and OneDrive still has the fundamental flaw around it's version control and deleting files. I still regularly do this:

1. Snapshot a virtual machine (or take an image of a PC)
2. Work on VM (or PC) for several weeks/sometimes months
3. Restore VM back (or restore image) to several weeks/months ago

Bang - restored version assumes it's master and randomly deletes new/newer files and/or overwrites newer versions with old. Had an example just last week. The folder that I install software from is in my OneDrive. Commissioning a new laptop and Adobe Acrobat failed to install - half of it's files missing.

This happens so often (i.e. nearly every time) that I'm totally paranoid about restoring VMs or images. I make sure I have backup of my OneDrive, turn the internet off, restore and then unsync OneDrive before reconnecting the internet.

In many cases, I also have Google Drive and Dropbox synchronising on the same computers. Never a problem with versioning...

My new storage location is apparently now the OneDrive Recycle bin. 40,000 files are send there per day. To think I just moved from GoogleDrive to OneDrive for my business. Next option is DropBox.