Hi @Reece, John
Is there a way to remove the sync'd/shortcutted items online?
As you said OneDrive online only has one shortcut visiable, other shortcuts seem not to be synced successfully. I suggest you do actions on local OneDrive folder directly.
Will uninstalling and reinstalling Desktop app change anything?
Does the Desktop app mean OneDrive client?
If so, you can try it, but I can not promise it will work for your issue. Thanks for your understanding.
Will unlinking the PC provide a solution?
I would like to suggest you unlink account first. Then please remove the shortcuts. This action would not affect the files or folders on OneDrive online.
For moving OneDrive on an external drive, please check out following references:
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