If you have a "recirculate" setting, use that to keep the water moving. It will bypass the filter and even going backwards shouldn't be a problem.

If your pool is vinyl you need to raise your pH to 7.0. You can use either Borax or Soda Ash (which will also raise your Tot alk which is low). Soda Ash is sold as Washing Soda by Arm&Hammer right next to the Borax. It's not baking soda--different, more caustic stuff.