Having sat in the audience and listened to my guitar (with a flapper) being played through a PA I think I know what you mean. It did seem to lose some resonance but the fundamental comes forward a bit which, to me, is not a bad thing. You couldn't detect all those overtones that you get playing unplugged but the sound was very discrete and penetrating while still retaining some acoustic ambience. Of course the guy playing it had a marvelous touch.