You can "undo" a distribution from an HSA. You can petition the HSA custodian to recognize the payment from the HSA that you made as a "Mistaken Distribution". If this is accepted, then you will need to complete a form (it's probably online at the custodian's website) and send a check for the amount of the distribution to the custodian. Note that the HSA custodian does not have to accept your request, so be nice. Explaining that you were unaware that you had insurance coverage in your case would be good (if it comes up). Once accepted, the HSA custodian will send you an updated 1099-SA.
For more background, please see "HSA Mistaken Distributions" on page 1 of the 1099-SA instructions.
In the future, if you have expenses that may be covered by insurance, try to run the bill through your insurance first, then pay the remainder from your HSA. If the medical professional demands full payment immediately, then pay the full bill using your credit card (or whatever), then run the bill through your insurance for reimbursement, and when you have finally discovered the remainder, ask your HSA custodian for a reimbursement for the remainder. That is, at any point in the future, you can ask for a distribution to you from the HSA to pay for medical bills, so long as the HSA was active at the time that the expense was incurred. (yes, even years in the future). This means that even if you don't have enough dollars in the HSA at the time you find out what the remainder is, you can continue to contribute to the HSA until you have enough money and then ask for the reimbursement.
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