Originally Posted by davidfor
Using calibre for this isn't very useful. It puts the annotations into the comments field of the book. There is no way to get them back to the device.
Are you sure the path and name of the epub matched what it was before? If they have changed for some reason, then the name of the annotation file will also change. The annotations file is created the first time you open the ePub. You can check the name of the file that is created and then replace it with the one you saved earlier.
When I copied them over, I got an "error" message for each one telling me there was already a file on the device with that name. In each case I told it to replace the newer file on the device with the older file that had been save to my computer before the device was reformatted. Was that right?