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The plugin will not retroactively work. After configuring (follow the directions, they are really easy but in-depth discussion is against forum policy) you should use Save to disk to save your calibre library. Then delete them from the library -- or the safe way is to Create new library -- and use Add books ==> add books from directory including subdirectories, assume each file is the same book in a different format.
You will retain all metadata, but the post-import hook will be run to activate the plugin on all books.
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