JWF, bacteria helps break down decaying matter like leaves, dead fish, etc. Bacteria will not remove what is left as it is essentially soil once bacteria consumes all it can...only physical removal/relocation will do that.

You might be shocked how little damage heavy equipment will do in the hands of a good operator, and frankly, a large track hoe is your BEST bet for getting a good sand bottom again, if it's there. Springs often bring in the sand, and if the pond has a spring in the bottom, there is probably a lot of sand in there.