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The annotations are saved in a database file ("{driveletter}:\.kobo\KoboReader.sqlite") at your KT. A copy of this file is also on your PC. In a windows environment, the path is something like "C:\documents and settings\your user name\local settings\kobo\". I have no idea why the complete synchronization has not taken place in your case. You might try to export the annotations (or to be more precice the respective entries of the table "Bookmarks" in the database) from the KoboReader.sqlite on your computer and add it to the KoboReader.sqlite on your KT. It will also be necessary to manipulate the time information in the respective entries in the "events" table to a recent date, to prevent the next synchronization to delete the bookmarks. Since I do not have my KT nor my labtop with me now, I cannot tell more.And what I said is rather guessing and might be inaccurate. I am sure other group members can help.
In any case it might be a good idea to save a copy of the KoboReader.sqlite of your computer before you attempt to synchronize via the desktop application or before you take any further steps.
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