When I tore down my dry biocube that I washed out first with a hose there was still so much gunk it wasnt funny. I literally washed it until I couldnt see any more gunk then cut it out and found that gunk got under silicone and into every crevice.
Depending on how much sediment was piled up, it could have also been a h2s release. That would kill pretty quickly, as I don't think that nitrate has the ability to kill that rapidly. (The median LC50 for fathead minnows is 1,341 mg/l, or TONS of nitrate to kill)
h2s release makes more sense. I don't know the chemistry of my tanks, I just know when something looks bad. My remaining fish has survived so things are looking up.