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Annotations is one reason why I was hesitant to switch to calibre. However, I decided the other benefits out-weighed it. Here is what I plan to do. I am going to manage my library with calibre. The Sony software has a feature that allows you to transfer books from the T1 to Reader for Mac/PC. You select the book and then click on the button called "Copy to My Library". I just tried it, and my notes were copied along with the book. So at least I can still export notes through the Sony software as needed.
You may not be aware that the Sony software has a limitation on the number of characters per highlight that can be exported to the RTF file. It is best to highlight in small consecutive segments. The maximum is 100 characters per each highlight in a DRM'ed book. It is ~200 characters for a non-DRM'ed book. The limit on the non-DRM'ed book is really small. In the old Sony software it was 2000 characters!
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