Some ideas to check........
Did you enter any 1099R? If 1040 line 4a is a lot less than 4b (which should be ok) the IRS has been lowering the taxable amount on 4b and refunding you. But then they will eventually want it back.
Did you make estimated payments and forget to enter them?
If you made estimated payments see if they are on line 17. Sometimes they end up line 16 with witholding. If that is the case the IRS will eventually see line 16 is wrong and ask for it back.
Check over your federal return and see if you can see anything wrong especially in the payments section. Check the withholding on 1040 line 16 for your W2 (box 2) and any 1099s you got (box 4). Or see if there are any estimated payments missing that you made and forgot to enter. Or did you apply your prior year refund to this year's tax return?
There may have been a mistake in the return, and the IRS just corrected it.
It could be the Earned Income Credit (EIC), or another credit. He should have (or be getting) a letter explaining the change.
If not, the only recourse is to contact IRS directly at 1-800-829-1040. Give yourself a lot of time, they're swamped now! And unless you have a Power of Attorney on file with the IRS, he's going to have to be the one who calls.