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Factory reset seems like a last resort that might not even help. This shouldn't be related to the jailbreak at all; it seems like purely a koreader issue.
First off, copy the entire koreader directory that's on your kindle onto your computer as a backup, as well as whatever directory your books are in. Your books and the files tracking your progress and notes will now all be in the backup. (I don't have time right now to figure out which files those are, but make a backup and hopefully I might have time to check later. Or someone else here can - or you can too: look around in the directory, maybe do a search for some words you know your notes contain or for the title of the book to see what files refer to it.)
Second, how did you reinstall? Did you first uninstall koreader completely and check that all the koreader files were wiped from the kindle, and only then install the correct version?
If not, try that. And then reinstall from scratch.
If you did, I'd try wiping it again and installing an older version (especially if you were previously using an old version that worked fine).
If things seem to be working fine, then you should be able to copy over your progress-related files and your notes from your backup to the new version (once you've identified which files those are). You can probably also copy over your settings files so that you don't have to set up any customizations you had before from scratch.
Finally, you may or may not have run into a bug. If no one here has more insights to the contrary, try submitting a possible bug report to koreader's github page with the error message you got and how to reproduce it.
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