I've updated my Kindle Store Proxy (https://github.com/pwr/KSP
). Last-read position and annotations are saved in KSP's database, so now deleting a Calibre book and re-downloading it will keep the last-read and any notes or bookrmarks you've made on it.
I've also tried to simplify the device registration process, though it still is somewhat involved.
Based on feedback I've received so far, I'm focusing on supporting more devices, in particular Kindle for Android, especially for the last-read position feature.