It looks like @dbshotgunn has provided the most practical solution to this situation, by combining the two different Box 12 amounts together. The IRS generally isn't interested in control numbers, those are for the payer's records. Since the income is non-taxable there would be no effect on your income taxes. This would allow you to e-file your tax return. As always, hold on to your records in case you need to verify your information down the road.
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