My experience with renovating ponds is that the fishery has suffered from the ill effects over a long period of time. In those cases, the fishery doesn't have much value at all. I look at it two ways. "If we keep these fish, will the fishery return to any semblance of health?" And, "What would it cost to replace them?"

In 90%+ of renovations, it's better to eliminate the fish, do a complete renovation, then let it fill with water and re-start. Takes less time, costs less money because the contractor doesn't have to move any extra dirt to save the few hundred dollars worth of fish.