I bought the Vigoro 'river rocks' from Home Depot and found out they are not inert (would raise pH). Might not be the problem, but thought I'd mention.
Some of those "river rocks" even had cement/concrete on them! (quite a bit too, no, no concrete on the bag, it was inside hardened to some rocks). There was many different types of stone and I'm no rock expert so I don't know which ones would be inert/safe.
It is said that the Hydrogen Sulfide pockets in anaerobic substrates are "instantly" "safe/nontoxic" as soon as they rise up into the aerobic/oxygenated water. I guess that is scientifically proven to be true, but I for one still believe there is something deadly that can build up under the substrate, some others agree as well, especially for those that have experienced or seen these events, but no one is 100% sure what it is. Some say disturbing the substrate can kick up decomposing organic matter and cause ammonia spikes. This is a whole big subject that I've been meaning to ask around on in hopes to finally get scientific answers as to possible reasons of sudden fish deaths when disturbing anaerobic substrates.
Do test your water as mentioned above. Even if you had to, take a cup of water from your tank and have your LFS test the water (some good LFS use the API liquid test kits, which is preferred over test strips). Knowing could possibly help identify what may be the cause of death.
Surely there must be some signs/symptoms leading to the fishes' death. Even if it was ammonia/nitrite poisoning, disease or even chemical poisoning, there would be some sort of exhibited signs before they die.