I'm sure you already know this, but I've "heard" that leaving sand alone for a long time (2 years in your case?) and then deciding to stir all of it at once might not be the best plan.I mean I really stirred up every inch of the sand with a turkey baster and watched all the stuff come up also I siphoned out my back chambers something I never have done like I did lol.
*I've always just used the sand vacuum as my water change -- I know others prefer to never touch the sand but to each his own