One inch equates to about 180 gallons so it sounds like you have a good size leak which should be easy to find. I doubt it but I guess there is a possibility that when you filled the added pressure could have caused something to let go deep. You're doing all the right things and looks like you've done your homework. With the dye you have to go really slow to avoid turbulance. When I was hunting down my leak I used a long piece of auto vacuum hose taped to a 1/2 or 3/4" PVC pipe and jury rigged the hose to a garden sprayer full of dye. I'd position the hose end where I wanted, let the currents die off, then give a little squirt of dye. Patience, patience, and more patience. When you get to the leak it will be obvious. You're lucky to only have to work in 4' of water. My leak was 8' down. If it is the liner have you seen my patching technique? If not I'll hunt down the thread.
Good Luck.
Al
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