I've never used dye myself as well. Some of the golf courses around here use it in their ponds, and it is supposed to suppress the growth of algae. My wife doesnít go for the look and so it will never fly here, heh heh.
Canít say Iíve ever run into a ground water problem, but conceivably that could happen in a marshy area. If your pond is in a low spot, runoff from the surrounding area could percolate down beneath the liner, orÖ and this can happen anywhere, as it did to me at my own place, if you have a break or disconnection in the output from the pump. My wife, bless her heart, put the pump back in the skimmer box in the spring, but didnít secure the fittings. Quite a bit of water Ė somehow Ė managed to work beneath the liner. I have an overflow French drain system and that area got soaked while much of the stones, gravel, and boulders along the side of the pond worked loose. But, this isnít directly related to draining the pond, but is something that could happen anytime to anyone who takes their pumps out for the winter.
I have clients who routinely want their ponds drained and cleaned out. It can be a lot of work, and my main concern is not to damage the liner Ė if it is a liner. Oh, and you will find different views on whether to clean or not to clean biofilters as well. Some people say that they clean theirs once or twice through the season; others say never to clean them because of the destruction of the beneficial bacteria. This year I didnít clean mine, and canít say if I noticed any difference Ė good or bad.
By the way, I just spotted in the local paper where some place is giving away 55-gallon drums for free. These make great inexpensive biofilters for koi ponds. If you can hide something that big Iíd suggest it. Oh, and make sure you have some bio start, or other type of starting bacteria, to jump start your pond in the spring when the water temp goes on the upswing.