As you have probably seen in other answers, you should make an entry on Schedule A that matches the HSA distributions, to offset the automatic transfer of the distributions against medical expenses on Schedule A.
For example, near the end of the Medical Expenses interview, you can enter a single line item called "expenses reimbursed by HSA" with the amount from the 1099-SA(s).
You are correct that some of the HSA distributions might have been for prior year expenses. And you may think it incorrect to show medical expenses on Schedule A for prior year expenses, just to offset the HSA distributions.
But the fact is that this HSA entry on Schedule A is not going to be part of the return. All you are doing is adjusting the medical expenses entered to compensate for the HSA distributions so that the final Schedule A number will be correct.
Since TurboTax does not know how much of the distribution was for a prior year, it just subtracts all of them on Schedule A in the belief that you will compensate appropriately on Schedule A.
Go ahead and enter the compensating entry as an other medical expense in Schedule A with the total amount of the HSA distributions in 2017 (for all years) - your return will be correct.
If you are concerned about doing this, just keep notes of why you did what you did in the very unlikely chance that the IRS will ever write to ask about this.
