If either spouse has an FSA, then both spouses are disqualified from contributing to an HSA. The tax consequence is that the HSA contributions are added back to taxable income. (A deduction is not allowed.) there is also a 6% penalty on the excess contributions, but the penalty is charged on the amount of excess contribution, or the year-end balance in the HSA, whichever is lower. So if you spent all the funds in the same year, you will not actually be assessed the 6% penalty, you will only be assessed income tax on the disallowed deduction.
