I may be misunderstanding this response here but it seems that this link's response contradicts yours.
https://ttlc.intuit.com/community/retirement/discussion/aren-t-hsa-contributions-pretax-why-does-my-...
From what i gathered, after you enter when you contributed and verify that you do indeed have a HSA and all purchases were tax deductible, at this point, you will then see the refund go back up.
