I turned the flanges on my MiniTrix Fs without removing the wheels from the axles, simply because I COULDN'T remove the uninsulated wheels. at least with the tools I had. What I did was to slide the insulated wheels in far enough to chuck the exposed axle end in the Dremel, then file that flange, being very careful not to damage the gear. Take the insulated wheel off, chuck the axle up to the gear, then file the uninsulated wheel. Finally, replace the insulated wheel and regauge. No micrometer, I just eyeballed the flange using the NMRA gauge. As long as it's shallow enough to clear the spikes, rounded on the bottom, and not so thin/sharp that it picks points or frogs it's good.
In my case I wanted to run them on ME code 40 flex, so the flanges had to be very close to the NMRA gauge. For code 55, a little deeper shouldn't hurt.
