Sorry, I'm here!
The problem you've got is that there is no program similar to EPCRS for nongovernmental 457(b)s.So you really can't get an answer, until and unless there is an audit.
The amount should have been reported on the W-2 in 2009. However, given that both the statute of limitations will have passed on both the employer and the employee, I don't know that you need to do anything about that now.
One question is whether you now pay him only the amount that should have been paid in 2009, or some kind of earnings since then. Payment of the earnings could generate a new reporting obligation.
As for the plan, in theory the IRS could go after it, but I doubt it would. It's not like a plan with a trust fund, in which tax benefits have been accruing to the plan all these years (due to untaxed earnings on account balances). In the case of a nongovernmental 457(b), the plan for each employee is more or less self-contained. (The tax consequences of one plan for each employee, or one plan for the whole group, would be identical.) So it wouldn't make sense to remove the tax benefits to current employees due to something that happened to a different employee back in 2009.