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I have had exactly the same problem with notes/annotations. I contacted Sony customer support in the UK and was told (after many emails) that the software was designed to work like that. Which sounds ludicrous to me! They stopped corresponding with me after I pointed out that it would only take 16 syncs to turn a single not/bookmark into 32768 (2^15)
I suspect this may be the cause of the ContentManager crashes I've seen mentioned on several forums as once I stopped using the sony reader software and reset my ereader everything worked fine again.
If only I had the programming skills to create a decent piece of sync software I would!!
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