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For what it's worth, I was having the same issue. MOBI files show up, AZW3 files weren't showing up all of a sudden, even though I've been loading them for years. AZW3 files showed up in the directory structure, but wouldn't appear on the Kindle. I submitted a bug request with Calibre and I was told immediately that it was an indexing problem, which I knew it wasn't because I had already checked that.
Turning off the wifi seemed to solve the issue for me. I've historically had it turned off but had it on this time. I don't know why that makes a difference but I guess I will have to remember to turn it off before side loading books. I let the people at Calibre know.
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