This is the scary bit about the Elipsa: your handwritten notes within books aren't backed up anywhere; they are only on the device. And, as it says
right here, if you have to do a factory reset on your device all your notes are gone for good:
- If you reset or sign out of your eReader, you’ll lose your annotations and handwritten notes.
- Handwritten notes will only appear on your Kobo eReader and won’t transfer to your Kobo Books app or other Kobo Readers.