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Afaik AZW3 format is only supported if it is unprotected.
If all AZW3 files are allready in Calibre, converting them shouldn't be a problem at all. If you are doing this, just use some sensible output options for the PB like f.i.:
/Author name/series name/series_nr_title.epub
{author_sort}/{series}/{series_index:0>3s}_{title}
to presort it into a nice folder sorted way.
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