I was playing a game with my brother when the following situation came up:
I controlled a Crypsis (with 1 virus counter) and a Sacrificial Construct. I also had three tags, so I feared that my brother may try to trash my Sacrificial Construct. As a result, I made a run on one of his servers (HQ, if I recall correctly), and used Crypsis to break the subroutine on the ICE protecting the server. From there, Crypsis forces me to remove 1 virus counter or trash it. I chose the latter, sacrificing my Sacrificial Construct to keep Crypsis in play.
My brother claims that this is an illegal play, and that because Crypsis had a virus counter, the virus counter must be removed. I may trash it only if Crypsis had no virus counters on it to begin with.
I say that I still get the choice and can give up my Sacrificial Construct to keep Crypsis and its virus counter.
In the end, it didn't matter, because the card I accessed ended up being an agenda which gave me enough agenda points to win the game regardless, but for the sake of future reference, who's right?
PS If this situation sounds familiar to you, it is because my brother already posted this on reddit. I figured that I'd go for something more official, just to be safe.