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I think you will find it is related to the DRM on the file.
Because you have effectively altered the file, it now no longer recognises it as being the same file.
DRM is anti-piracy and in a way your Kindle is acting as if you have tampered with the file (which you have) and now refuses to recognise it.
If you really want the file with the metadata changes that you applied you will need to look into removing DRM, which can be quite daunting (and perhaps illegal).
Otherwise just put up with the Amazon DRM and metadata.
Brewjono.
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