When you disturb the substrate you kill off bacteria, pretty much, so I'd say you were almost starting all over with your cycle.
There are so many factors at play - it is really hard to do all the right things, and if you do, it is by accident because you might not even know what the "right things" are without having messed up in the past. Over the years I have made all of the mistakes, believe me, and that's how I learned, so I'm really sorry about your fish losses but in the end you'll come out of it a more knowledgeable aquarist. I think that's what keeps me here at AA - trying to help others through the rough patches may make up a little bit for some of my foolish mistakes!