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Just for the record I have had Calibre libraries backed up on OneDrive without issues so there is no inherent problem with doing so.
However to get OneDrive to work you need to be able to copy/move the Calibre library folder and its contents to the OneDrive area on your local HDD before it starts syncing to the cloud. I wonder if since the OP thinks his HDD is in trouble this may not be working properly?
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