I'm also on a well so I had water trucked in for my water exchanges. It also has the advantage that the pool is filled back up very quickly. I ran my low end down to about 12" of water so I was concerned that the liner might shift. Knowing I could refill quickly helped me feel better about the whole process. Keep in mind that your mileage may vary and that there is an element of risk any time you lower the water level that much.
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