on Ph 6 water for a time,they need to be well flushed.
In a closed system this will mean changing to water several times a day.
After a few days of flushing, I would add some Hygrozyme or peroxide to the water. There is something growing in the roots media pumps somewhere in the system that needs eliminated. you need to act fast or plan on staring all over after a teardown, and stearlizing

Daddy