I'm not a fan of shocking a well. It can cause serious, read expensive, problems with the water quality, pump, drop pipe, power cable etc.. But you shocked a water tank. If it is steel, it could be rusting due t the chlorine and that may be where the dirty water is coming from if not from dirt in the bottom of the tank. If there is dirt on the tank bottom, then it may get into the softener and through it after a regeneration.
If you didn't by pass the softener when you shocked the tank, the resin is probably ruined or at least damaged which will cause a loss of capacity.
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