It is due to the 5.16.3 update: Scribe no longer mounts as USB mass storage, and instead uses MTP (Media Transfer Protocol) for file transfers.
Calibre has an MPT client, but will need an update to copy thumbnails over MTP for the Scribe.
If you somehow have a thumbnail with the required name (e.g. one created for another Kindle), you can copy it manually.
Or you can send ePub to Send To Kindle service, and you'll have a cover that way.
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