Ok... you do NOT mail in the amended return until the original refund is received ... so did she get the original refund yet ?  Did she file the return yet ?  

She got the original, which was only the taxes paid. I won't file the amended until I understand that it won't generate a bill.

If the student filed as a non-dependent and received a 1,000 credit, it most probably was applied to her tax, which is why she received the withheld taxes as a refund. Only the "refundable" portion of the American Opportunity Tax Credit would be a refund. 

Look at the original 1040 for the education credit, it would be figured on Form 8863 and also be on Schedule 3 line 50.

Just because she didn't get a 1,000 refund does not mean she didn't get the credit.