@Noirtier: Could you install the second-last beta and run calibre in debug mode and do the fetch? I removed a lot of debug logging in the last beta. The second-last will show a lot of detail about how the annotations are merged and put into calibre.
I also need to know which books have problems and some detail about the problem. Hopefully, I can see what it going wrong from the log.
When you have the log, either attach it here, or upload somewhere and PM me the link. It would also be good to have the database from the device. From that I can tell exactly what the annotation look like. If you can supply that, that would be good..
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