Thanks for reporting. I will look into this next, but I just started a week-long vacation, so my Notenik time might be a bit limited for the next several days.
If I continue working on the affected file, a duplicate entry will show up in the sidebar list (but still the one file on disk) and I’ll be able to click on it with the mouse and keyboard arrows, but not navigate to it using Next in Seq or Prior in Seq.