I would suggest printing the tax forms to pdf and reviewing them. You will want to ensure that on Form 5329, the excess amount is appearing in Part VII on page 2. You could also test that the "No, we're not going to make this withdrawal" is computing your tax properly by changing the answer of a partial repayment to zero or $1. The tax impact should be the same.
If the software seems "stuck" you can always just delete the HSA entry and re-do that, rather than recreate your entire return.
