Source: Penn State University
Corn that will be harvested as silage, and was previously in standing water during the growing season can be of concern when it comes to forage quality and palatability. Bacterial contaminants and silt can lead to animal health and fermentation problems.
According to a Cornell University publication by Paul Cerosaletti and Dale Dewing, silt deposition on standing corn can result in greater risk for clostridial contamination, as the primary source of clostridium bacteria is found in soil. If silage does not undergo the desired lactate fermentation and undergoes clostridial fermentation, moisture levels can reach greater than 70%, the pH is typically greater than 5.0, and a rank odor can be detected. This type of fermentation also causes deadly botulism toxins. Soil-contaminated forage can also contain coliform and listeria bacteria.
Corn that has been flooded and has a large amount of silt deposition on the standing forage could be of less risk to animal health and improper fermentation if it dried down and is harvested for grain. If the silt is found only on the portion of the plant near the ground, consider raising the chopping height so soil particles are not integrated into the chopped forage.
A publication from Cornell University goes more in depth on what to look for with flood damaged corn and management factors to consider.