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Sigil differs from Calibre in its interpretation of the epub3 spec about the need for doctype tags, especially for epub2 epubs that use named entities. Calibre interprets the spec differently saying these are optional.
But having a proper doctype can not hurt so Sigil offers to fix that for you. But I doubt very much that this is in any way related to your rejection by Amazon at all.
Try running your epub through the epubcheck plugin and fixing any issues it detects.
The read up on the kindle guidelines to make sure you are not using things unsupported in kindle.
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