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Instead of using Check library to list and optionally delete files not in the library, to move/reimport/discard them, one could create a new library (check the box to use the current library structure, if you wish to preserve layout/custom columns), and use the second option in the Add books dropdown, to import books from a directory, including subdirectories, assue each directory is a separate book where each file is is the same book in a different format.
It will import metadata from the opf, and the cover.jpeg -- I am informed (today) that apparently it will not import the cover unless there is an opf. But that shouldn't matter here.
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