| Jhamil4ton: Don't apologize. This is very much on point. It is often true that on the boards folks assert perfectly valid principles, but do not teach how to implement those principles. Your situation is a good example. I apologize to you.
It is important to keep in mind that the goal in maintaining a koi pond is to maintain stability as well as prime conditions. Fluctuations are negative. When implementing any change in a pond, the method for doing it has to be thought through... especially in regard impacts on the whole system. JR has listed the likely sources of the flashing. I'd guess that ammonia levels have risen. I think the disruption of the pond is putting you through a bout of "new pond syndrome". This does not mean you did the wrong thing. It means we should have volunteered some advice on how to make the change.
First, a disclaimer: I am not experienced in koikeeping in four season climates, so my thoughts may not be applicable to your situation. Hopefully others will chime in with advice for four-season koikeepers. In the warm climate I know, the nitrifier community will be set back by the disruption, but will re-establish in a couple of weeks. In cool/cold seasons, some different approaches may be appropriate.
First, if the bio-filter is gunked up with debris, I would give it a gentle cleaning to get rid of the gunk with as minimal a disruption to the nitrifiers as possible. We want an active, healthy bio-filter operating. If there is none on the pond, it is time to get one and get it established first. This may need to be done a couple of weeks in advance to get nitrifiers established/re-established. Second, I would not feed for a couple of days. Third, I would do a couple of daily water changes to try to get the pond pH and hardness close to the pH and hardness of the tap water (or other source water) that will be used to fill the pond. On the day the rocks are getting removed, I would remove all fish to a holding tank. The water in the holding tank would be 100% fresh water. Then all rocks would be removed. Then all water would be drained/pumped out. Do not scrub the pond clean. You want to protect the slimy feel of the pond walls. Algae on the pond walls is an ally. That means you need to work quickly to reduce the amount of the surface that dries out. ...Hope for a cloudy day and start early before the sun is strong. The pond would be filled with fresh water with dechlorinator added first.(We do not want the nitrifiers surviving the disruption to be wiped out by chlorine.) Unfortunately, in many rock-bottom ponds there is little surface available for nitrifier/algal growth, because covered by the rocks. The pond wall surfaces are deprived of oxygen until the rock is removed. It will take a couple of weeks for the pond surfaces to be colonized if there is an active bio-filter, even if somewhat undersized. If there is no active bio-filter, it will take longer. Return the koi to the pond and don't feed until your water testing shows no ammonia or nitrite and some nitrate appearing. Then, feed lightly, gradually increasing over a period of, say, 10 days. Invest in some ammonia-binder, such as Ammonia DeTox (which helps neutralize some of the nitrite as well).
Currently you are suffering through the disruption and wondering how everything could go so wrong. You are heading in the right direction. Don't look back. And, keep in mind that if you had not gotten rid of the rock, you'd be going through health problems equal or worse to what you are experiencing.
Congratulations on crossing over to the "light side". | 
10-28-2006
And the next time (if there is one), you're not going to be scared to scrape and scope. Don
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