Although I have had no problems with Lionel's repair doing the repair, I have noticed slight paint scratches or other minor damage on shells and attached items when I get the engine back. I usually just rub it out or fine sand it down and touch-up or glue it back on.
Given the short turn-around, I guess they have too many repairs and too few repair techs to take proper care or glove-handle when handling the engines. They dont seem to treat your engines like they are their engines.
So I guess there is a trade-off when you want a repair by Lionel. That sounds bad, but I accept a complex electronic repair for a few handling blemishes.