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I use a plugboard to rename books in series, and don't have a problem with the books being recognised by calibre as being on the device. Fetch annotations also works.
Not sure if it matters, but I have "Read metadata from files on device" checked for the kindle device plugin.
I guess you could try to rename the metadata.calibre file on the Kindle, then restart calibre. Calibre will recreate the metadata.calibre cache file(I think it takes a while if you have a lot of books in the kindle). Hopefully this will make you see your books correctly marked as on-device/in-library.
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