The new server is actually present in release builds (using the appropriate debug commands).
But the current E-Book Viewer saves bookmarks and current location inside the ebook (EPUB only) as well as in the configuration directory in the file "iterator.pickle".
The configuration data saves it according to full filename so you will need to have the books in the same location on both devices... but as long as you sync that file, bookmarks will work across computers.
The config data is canonical, but if it doesn't have anything for that book and the book is an EPUB it will check for the inside-the-EPUB backup.
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