OK, so the box 16 amount is different form box 1 on your W-2 by something like your 401(k) payroll deduction?
How were you deleting the 8889? By going into Forms mode (TurboTax CD/download)? I am sorry, but I don't understand why you wanted to do this.
"I inadvertently double deducted $1,292 for HSA contributions " - How did you "double deduct" it? What exactly did you do (or think you did)?
Whatever you do, don't make changes for your 1040X using Forms mode. Everything should be done in step-by-step.
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