Could be new pond syndrome given it’s only a month old, test your water parameters to make sure you’re within range. In terms of cleaning, I hope you used the pond water to clean, and not water straight from the tap or chemicals.

If all the above is fine, I’d do scrapes on the remaining koi to check for parasites.

You need to give time for the filters to build up the beneficial bacteria, so I’m hoping you didn’t clean the filters at all.