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You can use the "Save to Disk" option in Calibre to export all the titles known to Calibre (including their metadata) to a new folder. Then you could decide where you want your new calibre library to be located, create an empty one there and use the Add Books option selecting the option to where it is assumed each directory can contain multiple copies of the same book in different formats.
You message suggested that you had simply tried moving books around manually within the Calibre folder structure. This will not make them visible to Calibre as this process does not add entries to the metadata database.
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