The water has hopefully found its way off of the fields. Flooding for greater than two days may reduce soybean yield by as much 20% compared to one-day flooding events on soils with higher clay content. Doing some quick math here, 20% from a field that typically produces 50-bu./acre soybeans is 10 bu. This is approximately a $120 loss ($12/bu. estimated price for fall soybeans). It is time to check the costs of your inputs to determine if you can put additional inputs into this crop. Fields where soybeans were submerged, covered with silt etc, will not recover, and those should be forgotten about. Working on the drainage issues for that field, that will be money better spent.
For soybean fields with less flooding, we have several issues that are brewing, like soybean diseases to be scouted for. Here is another set of pictures to help in the identification diseases discussed, as well as photos of additional diseases to the ones here.