Sorry, no good advice in regards - except to note that I have tried doing exactly what you mention - I was trying to figure out how to backup notes - and failed as well.
the only way I found to backup annotations was to copy the documents to my PC using the Reader Library software and then backing up the Reader Library directories. Those can be restored. But, for some reason, the annotation directories are structured differently on the device - and I was never able to restore those.
Hope someone with more technical knowledge can solve your problem.
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