How much do you have underwater?

It depends.  IF that water receds quickly, probably not a lot bad is going to happen..... the longer that corn stays underwater, the more damage will be done.  the biggest concern is that the stalks and ears can/will become infected with molds and mycotoxins.  THAT is going to be the biggest concern.... and that is something you can't see, and probably won't realize until it is too late.  The other thing you might run into - and I am presuming that you are talking about shelling corn - is that you will have more dirt build-up .... there is going to be a lot more wear-and-tear on your combine as you harvest. and you will probably have more foreign matter in your corn sample.  But the biggest concern is going to be the mold and mycotoxin issue.