As of Calibre v0.7.44, the metadata changes required for "Furthest Page Read" syncing are now supported. When a book is converted to .mobi, Calibre automatically updates EXTH 113 & 501 so that Kindle and Kindle apps will sync your furthest page read across devices.
Now that Kindle for iPhone/iPad supports non-Amazon .mobi files, you only need to access those files (i use Dropbox or email the .mobi files to myself as attachments) on your iDevice, and you should be offered the option to open the file in Kindle reader app.
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