Need drain/refill recommendations

There will be some mixing, you just want to reduce it as much as possible. If the incoming water is colder than the pool, then fill at the bottom of one end of the pool and drain from the top of the opposite end of the pool.

It is hard to know how fast you are able to siphon and thus at what rate you can refill in order to calculate how long you would need to do it.

You may have to just do it for some about of time (like 15 hours) and then turn the pump on and mix it up and test to see where you are. There is a lot more guessing with this method than just a drain ~50% and refill, but I suppose it is safer.
 
Just wanted to followup that the simultaneous drain/fill worked great and was pretty efficient as far as I can tell. I wasn't able to get an effected siphon going, so I used a small pump I had which moved about 2-2.5 GPM and pumped from my shallow end while I ran the hose into the bottom of the deep end. It took 34 hours to drain ~5,000 gallons and i had my filter/sweep off the whole time. This successfully took the CYA from 80 down to 45. I would have gone longer, but I wanted to see if it was working, so I stopped and ran the filter to mix the water. Once I saw it worked, I drained an additional 1,500 gallons to bring CYA down to 40 (I hope, haven't retested yet). Thanks for the great suggestion. Now, on to SLAMing and OCLTs.
 
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