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What do you mean "the files contain both the old pdf as well as the new azw3"? calibre converts to AZW3, it doesn't embed PDFs inside the AZW3...
"I had to edit each metadata file individually" -- are you saying the library record had a PDF and an AZW3?
By default, the Kindle device driver does not transfer AZW3, since there are devices that do not support it. So if you only have a PDF and an AZW3, the PDF will be sent when using Send-to-device.
Go to the device configuration dialog (see screenshot) and make sure AZW3 is selected and heads the list for "Select available formats".
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