That is a feature of newer kindle firmware. If you have an AZW3 version of an Amazon-purchased book on your kindle it will automatically upgrade it to KFX format when you are online if that is available. This will enable enhanced typesetting and page flip, but will undo any customizations you may have made.
ETA: As a work around you could set your modified books to be personal documents (cdetype=PDOC), but this will have other side effects. The books will not show cover thumbnails on the kindle and your reading position and annotations will not sync between devices.
Last edited by jhowell; 11-13-2016 at 04:12 PM.
Reason: Additional info
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