I'm confused about my HSA 1099-SA... according to my W2, my employer contributed 1000.24 to my HSA. As of 12/30, the balance on my HSA was $0. but im told to withdraw??

My employer told me if I didn't show a $0 balance, I'd lose whatever funds I didn't use. So I made sure to use the last of the balance. Not sure how to proceed with entering this info bc Turbo is telling me there is a $1000.24 excess contribution and to withdraw it but it's already withdrawn???