From
https://www.mobileread.com/forums/sh...2&postcount=21
"if you want to backup annotations for epubs, you can backup the contents of the "Digital Editions/Annotations" directory. There will be a file for each epub that has been opened with the annotations in it. These can be restored to the device..."
I have previously successfully done this by replacing the newly created annot file with the backed up one after needing to re-checkout an expired library book.
The eReader.conf method certainly looks interesting too.