Nenn, I did take all the river rock out of the 180 gallon tank at once but I have the 90 gallon sump attached to that tank, with tons of marbles left intact in that sump as well as another wet/dry filter on the 180 with very large bio-ball capacity left undisturbed. So even though the river rock was removed all at once, not all of the substrate/media was removed from the system. I did expect a bump in the cycle. Nitrosoma colony is intact. I had a slight rise in ammonia for about 24 hours after removing the river rock and then it went to and has stayed at zero. But I have been registering 0.25 for nitrite for three weeks now, changing 100 gallons of water [of the 280 or so], every two or three days. Something kicked my nitrobacter colony in the pants... The only changes made have been removing river rock [again, only part of the media/substrate] and adding carbon to my filters. Theoretically, the nitrobacter colony should not have been wiped out, albeit their habitat was disrupted.The 0.25 nitrite level is not bothering my fish. Wakin are tough rascals and that is a relatively low dose of deadly poison <sigh>. But it is bothering *me*.

Our tap water registers zero for nitrite.
AH! One more thing I did was use a clarifier by Sea-Chem when I removed the river rock and the water clouded. Hmmmm..... Wondering if the clarifier might have zapped a good part of my nitrobacter colony. One more reason not to use chemical agents in our Goldfish aquariums is one never knows what the effects on the nitrogen cycle are going to be. I knew better. Quick fixes usually "ain't". Willing to bet the clarifier is the culpreit. Anyway, my other aquarium has zero nitrite and a normal nitrate level, so I transferred some media from that tank to the larger set up. Will see what's up in a week or so.
Thanks for your interest, Nenn.

Hope you're having a terrific weekend.