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And here's the bit I think wil put your mind at ease. When you upload to Amazon via KDP your file is run through a conversion process, even if it is in mobi/prc format. Uploading a mobi/prc is probably the preferred way to go nowadays, as it suffers almost no alteration from your source file, but it is still "converted".
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Just a bit of clarification. To my knowledge, uploaded mobi/prc files are not further "converted" by the KDP process. Since kindlegen (& Previewer) now produce a file that contains both the old MOBI format and the new KF8 format. Amazon will split the file into it's separate components so that they can deliver the proper format to the proper device (they don't deliver the whole uploaded file) and they strip the source from it (if it exists) before they deliver to customers. But otherwise, they're delivering the exact same mobi you uploaded to them. They do add some metadata and the DRM (if asked for), of course.
EDIT: that's with kindlegen-produced MOBIs. I have no idea what, if anything, happens to calibre-produced mobis.