^ So basically you left the original liner (which may have had problems) soaking in some water with salt + other chemicals which you aren't sure about, and hoping that once you rinse the liner off and re-install it into the pond that it won't effect the fish?
Honestly, i'm going to say its impossible to say whether or not your fish will survive... especially if you never worked out exactly what caused a problem in the first place... But with that being said, i guess there is a chance your fish will make it if all the equipment is clean and the water has been cycled properly, although even then you probably won't know for sure until you try it out?