Realistically the only way you can overwater in coco is if you have no perlite and lots of coco peat (coco dust fibers that are the size of coffee grounds). Many of us feed to runoff several times a day in coco. I think medidedicated feeds 12 times a day to runoff.
You spent half a day flushing the plants when they looked like shit. If the problem was overwatering, then they would have gotten worse after the flush instead of better. However, if the autopot was not functioning correctly and was pooling up water in the pots so that the roots were sitting in a pool of water, then that would cause it to be "overwatered."
Was it doing that? If so, then taking them out and doing a flush was getting them out of a pool of water and allowing the roots to get oxygen. Fully saturated coco will allow oxygen to get to the roots but coco sitting in a pool of water will not.