To enter a 1099-SA, you have to go to the HSA interview (under Deductions and Credits->Medical->1099-SA, HSA, MSA). Enter the interview, then when you are asked did you pay for anything out of the HSA, answer yes. Next TurboTax will ask you to enter the particulars for a 1099-SA. When you finish, Add another 1099-SA.
Again, what questions are you referring to that are not clear? I can't answer whether or not they reference your scenario if I don't know which questions you are referring to.
And you said, "but then found I did not qualify and the funds were returned to me." What funds? Are you referring to your HSA contributions? So were the 1099-SAs referring to amounts that were already in your HSA? If so you won't be getting a corrected 1099-R so ignore that.
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