After you file

You can handle the situation as discussed in the link by our wonderful Tax Expert @BMcCalpin,  printed here for your convenience. 

When you get reimbursed for something that you paid for with HSA dollars, this is a "Mistaken Distribution". What you need to do is this:

1. Contact your HSA administrator and tell them that you had a mistaken distribution (use that phrase). You may be able to report this through their website (go look).
2. Complete the mistaken distribution form and send it to the HSA administrator.
3. Also send the HSA administrator a check for the amount of the mistaken distribution.

The HSA administrator should send you a corrected 1099-SA to account for this "distribution".

You cannot convert money paid for with HSA dollars into personal money (like other family expenses) - these distributions are not only taxable at your regular income tax rates but you also are hit with a 20% penalty.  

The safest thing to do when you think you may get insurance or other reimbursements for doctor bills is to pay the amount from your regular checking account or credit card, and then after the insurance and other reimbursements come in, then you pay yourself for the unreimbursed amount from your HSA; that is, you contact your HSA administrator and asked to be reimbursed for unreimbursed medical expenses (they will send you a check from your HSA which you CAN use for family expenses). All this keeps the paperwork right with the IRS.

@CJ631