You can safely take it down to ~ 6" up the shallow end wall without worrying about having to reset the liner, actually 2" is the 'floor set' level but let's play it safe. Of course this is for a pool that doesn't have high ground water issues!

It's more efficient to drain as much water as you safely can to perform dilutions. If you suspect a ground water issue (like it's been raining for the past month, or all the local rivers are at flood stage) do multiple drainings so that you don't lower the water so much that the liner floats. Also be sure that your refill water is OK and won't cause you more problems.