Yes, if the 1099-Q was used for Qualified Education Expenses (including Room & Board), it does not need to be entered in any tax return.
If your student inputs the 1099-Q in her return, she does not have the corresponding Education Expenses to report (since you reported the 1098-T in your return), which is why her refund/tax due changes.
Here's more info on Form 1099-Q.
@nambuman
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