I hesitate to ask this but... what were you filing?
G.
what would one file to make a round rod (steer tube) fit into a round hole (stem?)
You need a picture?
I had thought that maybe you were filing the slot wider like TCBMX described OR doing something like this, but I was kind of hoping that you weren't doing what you did...
PLEASE dont run the stem like this, just warranty it.
If a stem has pinched then it has yielded. This goes for ANY pinch-bolt stem (or crank or brake lever or whatever), and ideally (in terms of safety) it should be replaced. In the case of Odyssey/Sunday stems we will happily warranty them (assuming that there aren't obvious signs of over-tightening abuse. Though to be honest if it has yielded like this then it has almost certainly been over-tightened, but we are pretty generous with the warranty).
Filing/sanding out the bore like this is a really bad idea. When the stem pinched the stem yielded and the hole effectively became larger (albeit with the slot closed up), by making it a bigger bore you are making things much much worse, it will now need to pinch closed even more to fit the steerer and the bolts on the back will be even more misaligned and likely to break and the stem will clamp less well and be more likely to slip.
I hope this makes sense and is helpful.
G.