Level 13

Deductions & credits

Money that was paid directly from your HSA (usually through a debit card) AND money that was sent to you to reimburse you for medical expenses that you paid out of pocket are both reported (together) on the 1099-SA that you received from the HSA administrator.

In your case, the important thing to do is to be sure to finish the HSA interview and indicate that all expenses were for qualified medical expenses (assuming they were). This amount would include both debit card payments and the reimbursed payments - which should match the amount reported as distributed on the 1099-SA.