You'll see this error message in the OneDrive sync app if a shortcut can't be synced:
Unable to sync shortcut
The folder <folder name> can’t be synced under <folder name> because it’s already syncing as a shortcut.
This issue happens when you have shortcuts to two separate folders, and then one folder is moved into the other. You can still access both folders on your PC and the files will continue to sync as expected, but you won’t see one folder inside the other as they show in OneDrive on the web.
To work around this issue, remove the shortcut to the subfolder (the folder that was moved into the parent folder). Once the shortcut is removed, OneDrive will sync the new folder/subfolder structure.
Right-click the subfolder in File Explorer and select Remove shortcut. Don’t worry—this will only remove the shortcut, not the folder or the content.