If the 1099-Q was completely used on qualified expenses, you can amend your return and remove the 1099-Q with the explanation that the 1099-Q was not required due to being fully used for qualified expenses.
Otherwise, if you have some portion that is taxable, you can make a statement about expenses not properly allocated as no education credit was taken or however you would like to word it. The point is to keep it simple to understand for whomever is reading your form.
Do not file the amended form until your original form is complete with any refund received. Be sure to note any refund or payment made with the original on the amended return.
You may need to amend your state return as well. See I need to amend my state return.
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