Let's do this.
A. Delete all your HSA information. Do it as follows (skip the W-2 part if you don't have W-2s).
1. make a copy of your W-2(s) (if you don't have the paper copies)
2. delete your W-2(s) (use the garbage can icon next to the W-2(s) on the Income screen
*** Desktop***
3. go to View (at the top), choose Forms, and select the desired form. Note the Delete Form button at the bottom of the screen.
*** Online ***
3. go to Tax Tools (on the left), and navigate to Tools->Delete a form
4. delete form(s) 1099-SA (if one), 8889-T, and 8889-S (if one)
5. go back and re-add your W-2(s), preferably adding them manually
6. go back and redo the entire HSA interview.
B. Now as you go back through the HSA interview (Federal->Deductions & Credits->Medical->HSA MSA Contributions), always indicate "none" as your coverage (like to both questions: "Was [name] covered by a High Deductible Health Plan (HDHP) in 2016?" or "Was [name] covered by a High Deductible Health Plan (HDHP) in 2017?").
You should get the excess contributions message and the fact that you can withdraw only a little, and that's fine.
This should get you through the Federal Review without incident. If it doesn't come back and tell me...
