Lines 16 and 18 of your form 8606 should show the net amount converted to a Roth IRA.
When entering your 1099-R, in the follow-up interview, there was a question Tell us if you moved the money through a rollover or conversion, then on the next page I converted some or all of it to a Roth IRA, you should enter the amount converted to a Roth IRA. You probably entered the gross amount.
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