First of all, you would need to enter this in the 1120 S return in deductions>retirement plan contributions. Then enter in Box 12 of his W2 as a code D. You will need to issue a W2C as MaryK1101 suggests.
Yes, you will need to amend the 941 because elective deferrals are always subject to FICA taxes.which must be deducted before deferring into the plan.
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