Chlorine kills it just fine, if you get the levels right.
But, are you using Baquacil? If so the only way we support Baquacil (PHMB) pools is by helping people convert from them, to chlorine.
Baquacil typically works well for a year or two, and then becomes a nightmare. You can avoid this by draining 2/3 of your pool every year, and by replacing your filter media (sand or cartridge) annually. If you haven't done that, and are using PHBM, there's no real fix.
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