If the leaking stops at 6" below the normal water line, the leak(S) are NOT pressure side piping leaks, and are NOT at the main drain or light. They ARE somewhere at or above the minus 6" level, possibly in or around the skimmer or tiles, but also possibly in the cracks. 2" overnight, on a 20x40 pool is ~1000 gallons per day, or about 0.7 gpm. Several small cracks can definitely do that.
I wouldn't use silicone; it tends to get nasty looking and not last very long. But, I don't know what would be best; others may.
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