Hi BorderReiver. I'm Greg, an installation specialist and 8 year Windows MVP, here to help you.
I root my User folders in OneDrive for some years now with no problems. If ever any are accidentally deleted they remain in the online Onedrive.com Recycle Bin even if the device's have emptied the recycle bins. If you right click Onedrive cloud icon in System Tray and from Settings dots choose View online, are the files in the Recycle Bin and how are they dated? You can order the contents by reverse date order to see easier.
But I'm wondering in this case if this isn't something to do with the new OneDrive on Demand where unless you tell it to save the files on the PC, it will only store them in the Cloud. You can check in OneDrive settings now: https://www.pcworld.com/article/3233488/windows...
What also might have happened since these are large files is you dragged them into OneDrive and they didn't have enough time to upload, yet were not set to be saved on the PC so they disappeared from both. If we can demonstrate this then it needs to be reported in Feedback Hub as a bug - this is where developers want this reported since they won't even see it here.
So choose to save Files on PC in OneDrive Settings, replace the files in the OneDrive folder, let them upload until they get the green checkmark. Good?
I hope this helps. Feel free to ask back any questions and let us know how it goes. I will keep working with you until it's resolved.
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