You got to do water change with each deflation, before he start to inflate again. Anemone deflates to purge themselves of bad stuff in them, most likely infection. If you we don't change the water (like in the ocean the waves carry the water away) their deflation is no good since they inflate and take in the stuff they wanted to purge back in.
I would start treatment, and make sure every time he deflates you change the water, and add antibiotic before he inflates if you can.