"Scripture references in the Bible view that have associated Study Notes will now display a wavy underline (in the Bible view). This is your reminder that a Study note exists for that verse."
Either all the refs are underlined or none are. Jn 3:16 has my study notes - but it is like there is no link from the Bible pane to the Study notes, no relation that connects to two by showing an underline.
Are there any toggles?
God bless you for this program. Amazing what it can do.