I'm siphoning the sand out using a pyton water changer so that almost nothing is getting released into the water column. I'm very much aware of how easily a tank can get nuked by changing out a sand bed on a running tank so this is a slow-slow process. I'm also working my way across the tank so that I can replace the sand at one end with new and allow it to get populated before removing the other side. Last thing I want is a more sterile sandbed than what i already have!
I agree with you about the deep sandbed though. I hae had one in my tank up til now and haven't had really any issues. It's only recently that it has become a problem and mainly I think it's becuase there was just too much biomass left in there from the die-off. I really should have flushed the sand out after I drained the tank and gotten rid of the stuff when I was cleaning it with fresh water.