I was discussing the issue of getting a non-original SSN, and the ramifications. In our home, two received a second SSN, but before their work years. (A lifelong PITA, having their original SSN "pop up" from time to time.)
From the employer aspect, my suggestion was not to question the new SSN, as long as the docs look reasonably good, but to just take it, and use it going forward. I would likely issue two W2 forms, one for each SSN, unless I found some regulations to the contrary. (Essentially treat the new SSN as a new "hire".)
Any here had to deal with this, two SSN used in the same tax year?