What I would do: (if $3,500 is not a significant portion of plan assets)
Put the $3,500 on the 5500 as a late deposit.
Pay interest to the trust (or to the individual account if applicable).
Submit form 5330 and pay the tax on the interest.
Notes:
I wouldn't change the W2, as the money was withheld from his paycheck.
No remedy under EPCRS for this.
No need for VFCP on this.