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I think the plants had taken over from the nitrifying bacteria and were removing most of the ammonia, thus starving out the bacteria.

Then you cut back the plants. In essence, removing your ammonia removal system.

The ammonia removing bacteria seem to have enough population to take care of an ammonia spike (maybe there was a small one and you missed it) but the nitrite removing bacteria cannot come back this fast, so there was a nitrite spike. The nitrite removing bacteria are slower growing.

Nitrite crosses the gills, enters the fishes' blood and alters it so it does not carry oxygen very well, resulting in brown blood disease. Add sodium chloride at the rate of 1 teaspoon per 20 gallons to reduce the amount of nitrite entering the fishes' blood. This is a very low dose of salt and is tolerated by all fish and plants. Other sources of chloride will work, too. Google Brown Blood Disease and include the word fish in your search to see what alternate sources of chloride you want to use and at what dose.
Keep up the water changes to keep the nitrite under 1 ppm.

Next time you need to prune, perhaps do it in 3 stages, a week apart, and leave more thriving plants to do biofilter duty.
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