Yes, he should be able to get his refund. However, it may be a good idea to mail in the return. Since for part of if not most of the year he worked under his old SSN, the W2s he received likely have his old SSN as well. If this is the case, mail in the return and attach a statement with documents that back up exactly what you post here. It may take a little while for the return to process, and the IRS may send correspondence, but in the end the IRS should be able to link your SOs income under his previous SSN to his revised SSN.
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