If you are worried about damaging the vinyl liner you could use a very large plastic sheet (the clear drop cloth kind you can pick up at any hardware store). You'll probably have to duct tape a few together to get the size you'd need to cover your pool surface plus 5-10 feet on all sides. That would act as a membrane between the old water and the new water and you could do a 100% water replacement without your pool ever actually being emptied.

Splash out/backwashing/etc. will lower your CYA...but not enough to make any kind of difference at all in your number.