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You are over thinking it. Use calibre to send files to your reader if you want to send files directly to sdcard and not use the ebook reader. Then you can use connect to folder option in calibre. Calibre detects what files are already on your device so you can dend only updated files later if you want.
Different readers have different requirements some will read the metadata but wont support series. Some will support folders so depending on the reader you get you can set up calibre to send files accordingly.
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