Quote:
Originally Posted by eschwartz
"Convert" in the subject field is for Amazon to convert the book themselves. calibre already sends a MOBI which your Kindle can read without conversions, so... no need to convert.
I have never known the email body to mess things up, and many many many many many people use calibre to email books to their Kindle.
Notes and highlights are completely different. If you've gotten that far, then your books were already sent, yes?
I don't think notes will be saved if you don't have the option in http://amzn.com/myk set to enable syncing annotations.
I am also not sure whether Amazon supports online viewing of annotations for Personal Documents, so that may not work anyway.
I'm not really 100% positive since I don't really pay attention to http://kindle.amazon.com 
Regardless, it involves the actions of your account once it has already received the book.
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eschwartz, yes that's correct. The books appear on the kindle and tagged as "personal".
As per
AmazonStrangely, unable to locate the option 'Annotations Backup' on the Kindle Paperwhite.
The solution I was looking for is for highlights and notes made to these books marked as "personal" to show up on kindle.amazon.com. I was under the impression, perhaps the body field in the email sent by Calibre is messing that up. Doesn't seem so.
Thanks for looking into this folks. Now that it's established that Calibre email isn't causing any problems, I'll poke Amazon support a bit more and see where it leads me to. Have a good one !