Before thinking about trying to remove the paint you should try to find out if what you have is a dealer repaint. According to the Greenberg guide to Lionel Trains 1945-1969 pp. 60 "Lionel marketing efforts suffered a slight setback in 1957 when the pastel Girl's Set was rejected by both girls and boys. In fact, many engines ended up being repainted black by dealers so they could be sold."
The problem is - I have no idea how you would go about determining if what you have is a dealer repaint.
