Ah. I found it. After my time, so I was completely unaware of it...
# 420.5n - If a permanent has both a +1/+1 counter and a -1/-1 counter on it, N +1/+1 and N -1/-1 counters are removed from it, where N is the smaller of the number of +1/+1 and -1/-1 counters on it. [CompRules 2006/10/01]...