Please clarify, did you report this as personal income on your 1040 or as Self-Employment on your Schedule C?
If personal, first enter the 1099-MISC
next go to
Income
scroll to the last option "Less Common Income"
scroll down to the last option there "Miscellaneous Income, 1099-A, 1099-C" START
scroll down to the last option there "Other reportable income" START
Answer "Yes" to start the interview
Type something like "Tax-free portion of medical leave" as the description and the amount as a negative amount.
The adjustment to income will show on your Schedule 1 line 8z and carry over to your 1040.
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