That smells like PEBCAK (and/or a bug somewhere that caused a reading state to be flagged as changed), as the plugin only cares about the reading state in the *nickel* DB, and KOReader doesn't touch that, ever (never ever ever!).
I should know, I wrote a
script to do the KOReader -> Nickel reading status update just so that I could keep using that feature of the Calibre plugin
.
(Said script requires my
Python distro; after which you can just 'right click > run python script' it in KOReader. I fav'ed it for ease of access on my devices).