Hi, there. I am the SharePoint Admin for my organization. I upload documents directly into the OneDrive shortcut regularly with no problem. I've encouraged our site owners to do that same, but it is not working for at least one of them. She has permission to Upload files directly to the site, and can do that with no problem, but when she uploads through the OneDrive shortcut, the file says it has been uploaded, but does not show up in the Document Library. I don't see any explanation for this.
Also, when we attempted to remove the shortcut from her OneDrive, she did not have the option to Remove shortcut, as I do. Only to cut or delete the file. We left it as is. I don't know if that means anything.