1611mac, thanks! I've been able to "extract" the annotations file from both isilo app and bluefire. Both files seen very promissor. Unfortunately, bluefire is crashing, freezing my ipad, 4.3.3, dont know why, so I couldnt test it better.
Im trying now isilo and Im not so happy with the reading there, but... If I can get my annotations out of thre, in a file that doesnt give me more trouble than writing, thatll be good! Ill let you know. Do you have any jailbroken idevice?