When you change the instrument or the tuning in the settings, it affects all the features like chords, scales, arpeggio, tuner or circle of fifths. But it does not affect all features. Some features like the songbook, chord progression or the fretboard trainer do store the tuning when the item (e.g. the song) is created. This means that you have the same tuning with the same chords and fingerings in a song, every time you open it. Independent from the instrument or the tuning in the settings. But you can change the tuning/instrument for a song or chord progression in the menu. Then the fingerings are changed too and the new tuning is stored in the item (e.g. song).