'I stir it up and vacuum regularly, but I want to suck it all out,'
Then there's no need. 2 years is nothing. Stop stirring.. let things break down. Just vacuum.
Why destroy most of your bio filter and reek such havoc in the tank, for nothing?
Do it if you wish to change the substrate or any practical purpose but not for the fish because better off left in peace,,, with just proper maintenance and feeding.