OK, so I have upgraded Calibre to 7.26 and DeDRM 10.0.9. When I plug in the device, I see lots of files, some of which are not marked as being in the library. I have been having to do the match book to library thing to get them connected* and I guess i forgot in the last batch of updates. If I do the Customize Plugin thing for eInk, I see two serial numbers, neither of which is my Paperwhite. Since for ages I have been doing the updates with the soon to be missing USB transfer, I guess it didn't need the serial number of the Paperwhite, but now it will, so I should add it. As for the warning about the cover, if the books are going from Kindle to Calibre, I guess this is not an issue.
* I suppose this is a difference in format issue and should go away with files now originating on the Kindle.
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