It's all good, it happens. Your help still made the tank better overall. The guy I talked to worked at OCA for over a year and said that anything over about 2" is prone to anaerobic things like hydrogen sulfite and that you don't want to do a deep clean on a bed like that. Surface yes, stirring the bottom, no. It's also where having something like a sand sifting star would prove beneficial (Which nobody had, BTW, so if you know of one for sale...).
Almost everything has died in the tank but I am taking it as an oppurtunity for a fresh start and also something to help others who might make this same mistake.