Absolutely. The employer, if performing as directed by the IRS, should prepare a W-2c for the year in question, and follow it up with a 941c or 941x. If the employee's portion of FICA/medicare is non-recoverable, the W-2c should be "grossed up" to include a phantom withheld amount for FICA/medicare. The employer will have additional payroll tax liability resulting from this, probably at least DOUBLE what he would have paid if properly filed to begin with.
Ever what state he is in also benefits by a probably increase in the SUTA tax - most overwhelmingly assessed against the employer as well.
The employee can prepare an amended 1040-X, claiming the new W-2 as wages, and subtracting of the gross amount on his schedule C. Expenses related to this amount should be reduced as well, and transferred to schedule A subject to 2%. (Assuming he included a schedule C on his original return.) Could result in a refund.
Of course, this predisposes that the IRS was correct in recharacterizing the income to begin with. They are known to be very aggressive in reclassifying payments to employee-status, and not very correct. Several years ago there was a list of "20 factors" that they supposedly considered, and then they abandoned the 20 factors because some of them gave powerful support to the other party. They would rather the decision be more subjective than directed by axioms, so they can be less accountable for their decisions.