There was no contingency plan in place for basically anything with regards to mishaps. Even the operations that did take place were full of snap decisions (the second bombing run is particularly full of such things, because things did not go as planned). So I don't think we have much of a basis to say what they would or wouldn't have done. It is of note that there was essentially no direction from "on high" regarding the second bombing, so whatever assumptions one might make need to be filtered through the fact that most of the decisions on that bombing were made on the island of Tinian (and not, say, Washington, DC).