I'm not sure that all Cholov Yisrael dairy producers do this; there have been a number of questions in the past about whether many dairy cows are treifa.
In a theoretical sense, we know that some dairy cows -- let's say more than 1.6% but less than 50% -- are treifos. If I have one cow on my farm, Bessie, then rov says assume Bessie is kosher, so Bessie's milk is 100% kosher. Okay I walk into a modern dairy setup with a thousand cows' milk all mixed together; if 4% of those cows are treifa, does that mean my milk is 4% treifa and 96% kosher? If so it's not kosher! Rabbi J. David Bleich writes about this in Tradition Spring 2008. The answer seems to be based on a ruba de-leisa kaman. If I don't know that any particular cow on my farm is treifa, even if I know that the general population in theory has a 4% treifa rate, then I assume each of my cows is 100% kosher, and thus the milk is 100% kosher.
So your question would only be if a mashgiach walks onto a dairy farm and knows specifically that there are one or more treifa cows here. Which I doubt is usually the case in industrial-scale chalav stam production.