Your idea of getting the stuff off and draining/ refilling sounds very workable. I'd take a test of the fill water for pH alk and hardness - sounds like the problem may be being exaserbated by the fill water, so if it is the fill water draining and refilling may not do any good If you don't mind the cleaning/ draining/ refilling and the fill water is good, it will probably save you a lot of time getting the water ballanced. If the fill water is ~ the same chem make-up as what's in the pool, you're going to want to drop the alk and run with a lower pH - it'll probably take quite a while to get the alk down and use a bunch of acid. Please let us know and we'll help you.
Oh yeah, be very!! careful!! draining a liner pool!!!! you should leave ~ 6" of water in it. If you don't know why I'm saying this, please ask for further info!

Best of luck with this!