I like the idea of taking a file to the wheels on a boxcar to create a real "flat spot", that would probably sound pretty real.
Actually not really, a friend did that some years ago and the sound was a puny, hardly heard "tink". A replacement wheelset cured that problem. That was done with a metal wheel in two-rail O with a metal hopper. BTW, the size of the filed spot was far bigger (when scaled up) than any flat spot on a prototype wheel would ever get.