Scott are you siphoning bottom, anoxic, nutrient rich layers? If so, should help with water quality issues [if any exist] when you refill later. Lusk/Eric often recommend removing a few feet of bottom water with siphon if one suspects quality issues...so that's going in your favor.
i actually have a separate pipe installed in the bottom of my pond. it is 4" diameter with the valve on the dry side. it runs straight thru the dam and pulls from the bottom/deepest point. i have a traditional standpipe and this 4" pipe is buried right beside it. so it pulls right off the bottom. the guy that built my first pond recommended doing that. it wasn't my idea, but i would suggest anyone building a pond to do it. it is so easy to just open a valve and pull bad water off the bottom, i have even opened it during a huge rain event to keep it from going over the emergency spillway.
