I periodically back-up the folders on my ereader too. I have successfully restored lost annotations from that back-up using the suggestions in this thread link.
https://www.mobileread.com/forums/sho....php?p=1368895
A few differences:
1) I don't modify the media.xml file as suggested.
2) I have found that you don't have to to paste everything between <text> and </text>. You will see for each book there is a tag called <markup> and </markup> where your annotations are stored. I copy & paste everything between those items from the back-up to my ereader.