It's not all about the Nitrobacter.
That's only one component of the baterial load. Perhaps there was a population of sulfer-reducing bacteria (for example) who were deprived of nutrients after the water change and began to die, releasing someting(s) toxic into the water too quickly to be tolerated.
This is only a general example. Bacteria are not all about the nitrogen cycle. There are other independent bacterial cycles present in a mature system. All of them matter.
There are also bacteria growing in/on plumbing pipes, on the aquarium surfaces, etc...which contribute to the water chemistry of the system. I don't know if you used the same plumbing or not, but it's a factor.
Even though you used the same rock, it's not the same system. What you did is not all that different from fully stocking a brand new tank in one day. I know, I did the same thing once.....ONCE!
I'm afraid that if this was the main factor, you'll never know exactly...for sure....what caused it.
I'd have to think real hard if I've ever seen a case where a one-day tank changeover went without a hitch. If so, it would be the exception IME.
I can't offer any proof that what I'm saying is the cause of your dilemma....but sometimes common biological sense is worth more than a test result.
The bottom line is that the foundation of a mature (assumingly stable) system had its equilibrium disrupted.
