@gsaxena2 reinburse yourself - it is your money, it's "use it or lose it".
When you complete your tax return, the $1,000 will be added back to your income (to reverse the deduction of your W-2 income) as you were not eligible for the FSA. Just answer the TT prompts - it will know you had the FSA because of the Code W in BOX 12 of the W-2.
