If you do not have a high water table problem, the low pH will definitely cause the problem that you have with your liner and there's not really any way to reverse it. The best way to deal with it is to try to move the wrinkles to the bottom of the wall (a toilet plunger works well for moving wrinkles around).
To avoid the problem again, you need to guard against low pH especially when you combine it with a high chlorine level.