@acouellette
"My employer contributed $5000 which I reimbursed to the employer" - Are you saying that you contributed $5,000 by payroll deduction to your HSA? If so, then it should appear in box 12 with a code of W on the W-2 (if it does, then good).
Technically, you didn't reimburse your employer; the IRS calls anything your employer contributes PLUS anything that you contribute through payroll deduction to be the "employer contribution", as confusing as that is.
As for the refund dropping, this is a good example of why you shouldn't watch the Refund Meter too closely.
Your employer removed the $5,000 from Wages in boxes 1, 3, and 5 before your W-2 was printed. This is the tax benefit of the "employer contribution" - it's never in your income in the first place.
However, until you show that you have proper HDHP coverage, the IRS considers the employer contribution to be taxable - that's why your refund drops, because the $5,000 is temporarily added back to income (line 8 Schedule 1 (1040)).
Once you go through the HSA interview and show what kind of HDHP coverage you have, the $5,000 will be removed from your income (become non taxable again), and your refund will go back up.
Take a deep breath and don't watch the Refund Meter so closely.
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