I believe what @MaryK4 is saying is to leave the form 1098-T entry off of your tax return, since it does not accurately reflect what happened.
That would be acceptable, however you may get a notice down the road form the IRS assessing wage income for the missing component where you paid back the tuition.
It might be better to leave the form off your tax return and submit a memo along with your tax return explaining what happened. You would have to mail your tax return in if you did this, however.
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