You should leave the medicare deductions off of the SSA-1099 entry. TurboTax will automatically pick them up as deductible medical insurance payments to be entered on schedule A for your itemized deductions.
Since they were reimbursed, they are not deductible.
However, most people don't itemize any more and even if they do, usually their medical insurance premiums are not enough to be deductible. So, it probably doesn't matter, but better to be safe than sorry.
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