Sounds like you are aware of all the possible pitfalls. One thing you might try is to drain and fill at the same time using a large plastic tarp to keep the new water from mixing with the old water. That would keep the pool from every being empty. You drain from the bottom and fill from the top. It has to be a big enough piece of plastic that it can extend onto the sides of your deck so that as the volume of the water increases on top, the sheet has room to sink without falling in and allowing the new and old water to mix.

I have never done this myself, but it has been discussed on the forum before. You may do a search and read some threads. Use the search feature in my signature below.