Tried it and you were right it worked. Good job by you to pick that.
This means Calibre solves both issues.
It seems instead of 2 errors it was 1 error (incorrect hyperlinks) that had 2 different outcomes depending upon whether the ebook had the notes internally in the main.html or as individual notes.html (eg note1.html, note2.html etc).
Updated wiki to reflect.
Kovid never rests on his laurels does he!