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OK, two things:
1) Kindle’s own UI and its Collections is not really useful for KOReader because Kindle can’t see and sort all KOReader- and calibre-compatible formats (epub, fb2, djvu, etc) and Kindle UI cannot open those books from Collections in KOReader anyway (there used to be a way many years ago, but it is not supported anymore).
2) KOReader’s File Browser where you select books is just that - a true file browser that shows all supported (or also unsupported files with a setting) files in a list, not collections. There might be a plugin that sorts for that, have a look at, say, Project Title or similar project on KOReader/contrib Github page.
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