I'm thinking it's your nitrates, myself. We'll know for sure when you post the readings later on. Huge water changes aren't as bad as many would lead you to believe, unless there are big differences in pH or temperature. I recently did a major overhaul/cleaning on my little 10g, as I had some staghorn algae taking over the tank. I ended up yanking out all the plants and tossing them, except for a few of the root feeders(gave them a major haircut)...then I preceeded on doing a series of large water changes while stirring up the gravel...which kicked up quite a bit of debris. The fish weren't too crazy about this whole process, but weathered it like the champs they are. I think I ended up running about 30g of water through the tank before it was all said and done...I guess that equates to a 300% water change..lol. Then I cleaned the filter very well, and took some plants from my 55g and replanted the 10 with those. The tank is spotless and very clear, and the fish and shrimp are doing exceptionally well.
So I really don't think your fish died from 'overcleaning' your tank.
So I really don't think your fish died from 'overcleaning' your tank.