what to do?

[Richer]

The bacteria that we want don't live in the water column. Most, if not all resign on the surface of your tank, rock, sand, etc. A large water change should not have a significantly negative impact on a newly cycled tank (assuming the water going into the tank does not differ significantly from the water that is leaving the tank). However, I would still suggest testing the water for a couple of days after a water change before adding anything to the tank.

-Rich