I just upgraded my Kindle, and am now taking the opportunity to send my non-Amazon eBooks to my Amazon documents so they can be accessed and sync between multiple devices (previously I had just loaded them directly onto the Kindle).

Converting to MOBI and emailing them to the Kindle address works, and WhisperSync keeps everything synced... with one exception.

If I remove one of these eBooks from all devices (it still remains in the cloud); reading position, bookmarks, and notes all disappear (i.e. if I redownload it to one of my devices to re-read it, all these things are gone).

This doesn't happen with books purchased through the Amazon store, only third party ones I email to personal document storage.

I've looked at all the settings and Googled it, but can't find anything.

Does anyone have any ideas, or is this just one of the downsides of adding non-Amazon books to your Kindle library?