Where are the smoke settings stored? Onboard in the engine’s electronics or in the Legacy control components? Thinking about it I suppose it would be the latter, in which case it seems to follow running the engine in conventional transformer-only control would have no impact on them.
I have noticed however that Legacy EFX settings don’t seem to be stored after an engine is shut down. I find I have to ramp them up again the next time the engine is operated. Not sure why that would be different from smoke settings.