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Are you using the epubcheck plugin for the calibre ebook-editor to check for errors? Send to Kindle is rather fussy over even minor errors.
The cover and .opf file are part of calibre's library storage and you should not be mucking with those files. If you want to embed cover and metadata information, you can either use calibre's Polish tool or install the ModifyEpub plugin. Normally, the epub file in the calibre library will not be modified unless you use a tool that does so. When you save to disk or send to device, the default is to embed metadata since those files are moving outside of calibre.
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