I encountered a similar problem just earlier. I sent an epub to Calibre Companion by USB and the Calibre "send to device" button, but it wouldn't show up in CC. It
was in my designated folder on my phone, though.
What solved the issue for me was that I disconnected the USB cable, and reconnected CC to Calibre via WiFi. Which was completely by chance, though. After finishing the scan CC always does, the books were in my CC with all metadata I assigned to it in Calibre

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I am not 100% sure if you tried it like that already. I did read your thread, dear OP, but I have to admit that it got very technical for my non-IT brain at certain points, and if I simply missed it, I apologise. If you didn't try it, though, it would be great to know if that works for you and/or anyone else!
It is not the quickest way, but it's definitely quicker than transferring epubs through my WiFi

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I'm on Win 8.1, Calibre is 3.44, and use a Samsung Galaxy 7 with CC version 5.4.3.3 (391). All programs and apps are up-to-date.