Joe,

AS long as you only drain about half your pool, the liner will be fine. As you drain, observe for any wrinkling or movement of the liner that might not come out when the water refills. If you observe something you don't like, stop at that point just to be safe.

I would suggest you refill completely and then shock. Your pump probably won't circulate once you drain below the skimmers. Additionally, you'll only have to shock once instead of twice