This one is somewhat difficult to explain, but its probably the most interesting feature of the Harmony Browser. Lets assume, you have a sequence of 4 chords. Then you select 4 bars in the track window (all tracks) and you press the transpose button. Now, the Harmony Browser tries to change the harmonies and scales from the trackwindow selection into the selected chords.
The algorithm looks at the first bar from the trackwin selection and sums up the length of all different notes. It assumes, that the 4 notes with the largest sum of length are the chords present in the song and changes them to the 4 notes from the first chord of your chord selection. Afterwards, the remaining notes from the trackwin selection are mapped to the remaining notes of the scale the chord was taken from.