Just wanted to give an update on this. We ran a drain king on the behind the liner drain and it was not blocked. I had a leak detection company take a look and they found a leak at the pool light. There was a crack in the conduit at the back of the light niche that was repaired with epoxy. I imagine the water was leaking into the ground and then behind the liner, causing the water to be unable to self drain back into the ground because of the constant flow of water back into the ground from the pool light. Kind of a never ending cycle.
I still thought the behind the liner drain would get to the water, but I think it was kind of "stuck" in place at the deep end and wasn't being pushed to the drain at the shallow end, as it normally does.