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I've noticed something similar, though in a slightly different setup. I use ascm files to download the books themselves into the Adobe Digital Editions app on my MacBook. Since I don't like any of the Adobe readers, I convert the books with calibre and read them using the native Books apps on my MacBook and iPhone.
Sometime later, I'll discover that both the original epub and the calibre epub have been replaced by a single mobi file. After reading this thread, I'm convinced that there's some automatic library housekeeping going on behind the scenes. This happens only to the epubs in my calibre library - the books I've added to my native Books libraries aren't affected.
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