Update cached metadata on device only affects the calibre "Device" view. If you have used the Match Books option (Device view, right-click menu) then Update cached metadata will rebuild the metadata.calibre file on the device.
As soon as you use Send-to-device the AZW3 file should be written to the Kindle drive.
Once ejected, the Kindle will find all ebook files on the drive, unless it is malfunctioning. But it may take a bit of time to index it, specifically if there are many new books and/or the indexer jams

.