Yes, this happened to a client of ours. long story short we filed an amended return for client's daughter, she owed about 13k on the 1040X. We could not e-file because original return filed in different software. So we mailed it in and told client to pay the 13k for daughter, and he did so electronically. 

a couple months ago dauughter received a refund check for 14k and has no idea why. We tell her not to cash it and hold on to it. 

She signed 2848 so we can call practitioner hotline. turns out even though return was mailed in October, it didn't post to account until May and has not even been processed yet. And payment hadn't been processed until April even though sent simultaneously with return (in october). lol

So we were instructed to mail the check back to some "refund inquiry unit" in Philly, write VOID on the endorsement line, and include a letter with a short explanation of why sending back. 

I suspect it will be the same situation with your client but you should call the hotline first to verify. perhaps there is another issue. 

the number is 866 860 4259 and choose option 2. make sure you have a signed 2848 on file or ready to fax.