Whenever one house of Congress significantly alters a bill: the bill is nullified. the chief justice determines the constitutionality of the changes. the president vetoes the bill. a conference committee is formed to reconcile the differences versions of the bill.
I am going to take an educated guess and say the last one because just because a bill changes I don't think it would be nullified. Also I don't think that the chief justice has anything to do with the Congress and their decisions unless it has to do with the law and it being unconstitutional. Furthermore, just because their are changes does not mean that the President is going to automatically veto the bill, he has to he it first after the congress is done with it, so ultimately the last one makes the most sense.
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