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I did not enter it as a negative value in a 1099 yet I have a subtraction on Schedule 1, Line 8 of my Form 1040. I assume this is because I selected Code II for Box 12 of the W-2 form. So based on what you're saying, if I keep the value in Box 1 of W2 and Box 12 then the negative value in the 1099 would have to be double (the total of Box 1 and 12), to prevent being inappropriately taxed. I think that's also what the IRS website says below. [If box 1 is not zero]..."report the box 1 amount on Form 1040 line 1a, and the box 12 Code II amount on Form 1040 line 1d. Then, on Schedule 1 (Form 1040), line 8s, enter the total amount of the nontaxable Medicaid wavier payments reported on Form 1040, line 1a and 1d, in the entry space in the preprinted parentheses (as a negative number). " https://www.irs.gov/individuals/certain-medicaid-waiver-payments-may-be-excludable-from-income