I read though the write up on doing the acid cleaning and one thing it said was that the filter should be in recirculate mode to bypass the filter while cleaning. It said that flowing though the filter could cause problems. So I followed instructions and put the filter in recirc mode. However, I also wanted to rid the filter of any iron that could get back to the pool. So my solution was to put the filter in backwash and allow it to flow until the backwash water was completely clear. Then with the pump running and the filter in backwash I added 1/4 cup of AA to the skimmer, counted to 10 and shut the pump off. After 1 hour I just jogged the pump by turning it on for 2 seconds then off again. After 2 hours I repeated the jogging. At three hours I turned the pump on and watched the backwash water coming out. It was clear for several seconds then turned tea colored, then blood red. It ran blood red for several seconds, then tea colored, then cleared up.
That was an eye opener for me so I repeated the whole sequence. The second time I didn't see any discolored water after soaking the filter for three hours.