The notes from the arpeggiate-command, (A47) for example, do not change when a certain scale is selected in the Instrument.
So if you have a phrase with C-A47 and set it to C-Major you can’t play A#, but if you play A you still get A-Major and not A-Minor. (Because the Arpeggiated command does not adjust to A37, etc.)
Hope this helps, cheers.