The repayment of a scholarship is not a qualified education expense and is not tax deductible.
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The 1098-T is only any informational document. The numbers on it are not required to be entered onto your tax return. You claim the tuition credit, or report scholarship income, based on your own financial records, not the 1098-T.
At the 1098-T screen, change the numbers to whatever you need to meet your records. It sounds like you just need to change box 5 to 0 (or leave it blank). You, not scholarships, effectively paid the tuition.
Alternatively, in the 1098-T screen, click on the link "What if this is not what I paid the school" underneath box 1. You will then be able to enter the total actual amounts paid.