John,
Some questions for now. Do you know if the water level stabilized at 2" at the shallow end? All your plumbing should be above that level unless you have a main drain. If you don't have a MD then it's a liner leak or....how about stairs into the pool. A common leak area is the pinch of the liner around the stair opening. In my opinion the first step in your case would be to fill a few inches and see what happens. Measure the depth accurately at some known point to be able to estimate a loss rate. Depth change x surface area to yield cubic feet per time then gallons per time. Then we can go from there. 'Typically' the greater the depth to the leak, the faster the water will leak. Eventually stopping at the depth of the leak. Last year I developed some techniques on finding and repairing leaks for my own problem.
Al