Thats wild that the when you reviewed the return with the client, this was missed.   Didnt they wonder why the refund was so high?

At any rate, your only option is to amend, but you have to wait for the return to complete processing first, which means wait for the refund, then pay back whatever the difference is with the amended return. 

1040X isnt ready yet anyhow, I think its got another week or so.