yep. in theory if the CEL flashed you should have a "pending code". This should show up on a scanner.
However, my cheap ass scanner doesn't seem to show pending codes even though it claims it does, I've had a similar situation to yours. CEL flashed, went to scan it--and nothing...
Probably not a great method, but I actually try to make mine run rough or replicate the problem to see if I can get it to throw a real CEL. (I have a misfire that only seems to happen at a certain RPM so I actually hold it there until it knocks enough to throw the light)