I have not reviewed the medical expense interview for this season, but in the past, the program asked you for all your total expenses, then separately asked for any non-taxable payments or reimbursement (such as HSA, medical insurance, HRA, or other type of non-taxed reimbursement). Turbotax does the subtraction and reposts the rest as the deductible amount. In other words, it wants you to tell it everything and let it do the work.
That being the case, if you don't tell Turbotax about the expenses that were covered by the HSA, you should also not report the HSA. But since you have to report the HSA from form 1099-SA, the program cross-references that to the medical deductions. So you need to enter your total expenses, to be counted against your non-taxed reimbursements.
