Originally Posted by melabonbon
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?
That should have worked. The message tells me that the annotations file was already there and you replaced it. But, that doesn't make sense. If you did a factory reset, visible partition on the device is formatted. After a factory reset, the annotations files only get created when you open an epub or PDF.
I would suggest going through the saved files and finding one that definitely has annotations in it. It is a text file containing XML. You can open them in a text editor. The first few lines show the book it is for, then there will be a"<annotation>" tag for each annotation. Once you find one, make sure it has been copied to the correct place on the device. Then, disconnect the device and test the book. If the annotations aren't there, add one, close and reopen the book to check that it is saved. Then connect the device and check the annotation file to see if the new annotation is there. And it is the name expected.
tshering's idea of checking the saved database would help check what books had annotations before the reset. Putting it back on the device might work, but it is likely to put you back to the same point you were before the reset. You could extract the annotations from the database and insert them into the current database. But, I have tried this in the past and it didn't. My tests show that, the annotations file takes precedence. Whatever is in that file will be read when opening the book.