Yes changing aircraft mid flight will shut your engines down, like most new releases that have advance coding ie PMDG, Cerasim & A2A the engines will shut down when swapping models. Its a trade off for abilities of the aircraft, sadly there is nothing you can do about that
What config change are you worried about? the "HIGHMEMFIX=1" entry? its one of the more nessesary fixes for your fsx.cfg these days, not only does milviz recommend it, but many developers and tweaking sources do as well including many members here.