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I don't use the desktop app, but the mobile app has a setting for what to do with the original file:
I have different sync folders setup differently depending on use case, but I typically use option #1 as my "default".
Maybe when you setup the sync folder, you set it to delete the local files?
Also, is the OneDrive folder a "real" folder or virtual one? I've only used Google Drive for things like that, and the local folder just holds a skeleton of the contents and pulls from the network on-demand. It...does not play well with other sync utilities or even copying through robocopy.
OneDrive uses virtual files and there is an open bug that isn't getting enough attention
https://feddit.it/comment/10231887