"Our son graduated, became employed, and will not be our dependent for 2024 tax purposes."
All of that is irrelevant for your situation. The beneficiary of the 529 plan does not have to be the owner's dependent.
The re-contribution to the 529 plan must be within 60 days of the distribution or within 60 days of receiving a refund from the school, to be valid.
So, the answer depends on why you got the refund. Was it a refund of the scholarship or a refund of the expenses you paid. If it's a refund of expenses, your 2023 distribution is still considered a qualified distribution and you don't need to do anything. Likewise, the student can consider the scholarship money as having paid for tuition (a qualified expense) and it is tax free.
If it was the scholarship that was refunded then you need file an amended 2023 return to report the non qualified distribution or your son must treat the scholarship as taxable or a some of each. You may have to do math to determine the best outcome for the family. Although you may have to pay tax on the distribution, you qualify for the scholarship penalty exception. The distribution amount (box 1 of the 1099-Q) is not the taxable amount. The taxable amount is the earnings in box 2.*
That said, you only mention the 2024 tuition expense. Room & board, books and a computer are also qualified expenses for a 529 distribution. You cannot count 2024 R&B for a 2023 distribution, but you can count 2023 R&B. Books and a computer, paid for in 2024, are qualified expenses for the scholarship.
*Example: Box 1 is $10,000, box 2 is $5000. Because of the $6000 scholarship, only $4000 of the box 1 amount is now qualified. $6000 is a non qualified distribution. 6000/10,000 = 60%. 60% of the box 2 amount is taxable. 60% x $5000 = $3000 taxable income on your 2023 return vs. $6000 taxable scholarship on his 2024 return.
