I've wondered about this as well. IMO (correct me if I am wrong) if you drained the loop there would still be a little bit of water left over. That combined with the fact that when you drain it there will be new air (with bacteria, microbes, etc.) that has now been introduced to the loop. That stagnant water in the loop is now being exposed to outside air would only lead me to believe that it could potentially start growing some funky stuff. The next time you put in fresh water it would contaminate it. If that makes sense.
I say leave the water in there now since as far as you know it is sterile.
If you have dye I would drain it and put in regular distilled for the long break and make sure to use a kill coil or something of that nature.