Calibre certainly can store ebooks with DRM in them, it just can't view or edit or convert, but it can Send the file via USB to the Kindle or ADE authorised device that the file is keyed to and then they are readable.
However I'd not bother putting borrowed/library books into Calibre. There is no point with KU (as they can't be downloaded anyway) and it's too much bother with the library books, I just use the Library app on an Android eink (no Overdrive for Kobo).
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