Being covered by the HRA for the entire year makes you ineligible to contribute to an HSA for the entire year. Your HSA contributions are therefore excess contributions that are subject to a 6% penalty every year that they remain in the HSA. To avoid the penalty you must request an explicit return of the excess contributions before the due date of your tax return, including extensions, (not a regular distribution) for the year for which the contributions were made.
Failure to obtain a return of excess contribution by the due date of the tax return will result in the contribution not being excluded from your income and continued penalties each year that the excess remains. To eliminate the excess after the due date of the tax return you would either need to be able to apply the excess as an HSA contribution in the future when you are eligible to contribute or to obtain a taxable regular distribution from the HSA. A taxable distribution to correct and excess contribution is one that is not applied to qualified medical expenses. It means double taxation of that money (because that money was not originally excluded from income) and is subject to a 20% penalty if made before you reach age 65, so you really want to avoid having to do that.
