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I am still a bit confused - if you have the metadata.db file and all the folders containing eBook files at the same location then simply pointing Calibre at that location is normally all that need doing to see the books. You imply that there are empty book folders at that location - but I thought you had just copies folders containing books to that location?
The other possibility is that the metadata.db file at that location is damaged. If that happens then you may not be able to see you books in Calibre. The normal answer to this is to restore the last known good metadata.db file to this location (the eBook files should still be there) and restart Calibre. In that case you would lose any changes made since that backup was made.
I do not see mich point in reporting this as a bug as I do not think there is a Calibre bug. It is just that you have got something corrupted on your system that is causing all your problems.
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