$5000 seems a bit high to me, but I haven't ever had to replace mine. In looking around online, $2000-$2500 seems to be an average price for a liner that size--I guess the difference is how much your installer charges to install it. I'd shop around. I'd also have the installer put in writing that you "will not have any problems draining the pool". If it weren't a possibility, then he wouldn't have the clause in the contract that states that he's not responsible for any damage that may occur from draining it.
I also strongly disagree with your installer about the chlorine issue. Ponds, creeks, and other small bodies of water have developed biological climates to maintain balance between fish, plants, and bacteria so that everything thrives. That climate is easily disrupted, and 20K gallons of chlorinated water would do a good job of it.
Janet
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