there are several ways tuning is controlled in your Stage, at different levels:
1- global tuning in the Sound menu (check the manual for details). Set global tranpose to zero (or the desired amount if for example the band's guitars are tuned 1/2 step down)
2- each specific program tuning, controlled by the transpose button. Check if the transpose light is on, and turn it off and/or adjust the amount.
3- every part (organ, piano and synth) has its own octave setting, controlled by the octave buttons right below each part's Level knob
4- specific to the synth section only, the oscillators may be detuned. This is controlled by the Shape knob when in Detune (Dtn) mode, check the manual for more details.
Still, it seems very odd that your son was able to permanently change the tuning of so many sounds, because he would have had to save them afterwards, or the changes wouldn't have been retained. Has the instrument been turned off after the accident? If not, and if nothing was saved, the simplest solution may just be to do a power off/on cycle.
