Yes, you probably need to file an amended return. If you didn't include your 1099-SA on your return, then you wouldn't have reported the amount of distributions from your HSA that were for qualified medical expenses. The information reported to you on your 1099-SA is also reported to the IRS. The IRS matches up all information reported to them with what taxpayers report on their tax returns. Since you didn't include your 1099-SA they will propose making an adjustment to your return that adds the distribution, but not the amount of it that was spent on qualified medical expenses. They will send you a letter and proposed additional taxes, penalties, and interest. If any of the payments/purchases you made with your debit card were not for qualified medical expenses then those amounts are taxable and subject to a 10% penalty. You can wait for them to do that (it could be more than a year) or you can resolve the issue now by filing an Amended Return.
