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I use calbredb as part of a script to extract my epubs to a single level folder and my azw3s to another:
calibredb export --progress --all --dont-save-cover --dont-write-opf --format epub --single-dir --template "{authors}-{series}{series_index:0>2s|[|]-}{title}" --to-dir <destination folder goes here>
Then I can just side-load onto my Kindle
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