When in Melody mode, the big piano keyboard does not act in the same way as in the other modes of the program.  For one thing, dragging the mouse pointer on top of it while holding the left mouse button down does not affect the selected chord keys.  For another, right clicking on a keyboard key while pressing the Ctrl key adds a melody note and adds the chord to the chord table.

To clear the chord notes use the key.

The first time the key is used only the chord notes are cleared.  The second time the melody note is cleared too.