If you followed the steps from this thread, using the entry field provided to deduct interest from the amount shown on Form 1099-INT, then entering a positive number should reduce the taxable interest.
If you made the adjustment by another method, such as creating a separate Form 1099-INT, instead of in an entry field that is provided in order to deduct from interest, then yes, you would enter a negative number.
Please also see IRS Publication 550 for more information.
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