@dmertz
This has been a very informative read, but I do have one question:
For my situation, my spouse and I are both on the same family HDHP, and I had $6000 contributed from my employer payroll, of which $3000 was payroll contribution to my HSA, $3000 was payroll contribution to my spouses HSA. My W2 Box 1 excludes the combined $6000 and the W2 Box 12 code W has the combined $6000 listed. From what you state above and from what I understand from IRS Notice 2008-59 Q-26, the amount in W2 box 1 should be corrected to include the $3000 that went to my spouses HSA. I would then include this $3000 as a deduction on Schedule 1 line 13 as you mention.
However, given that the W2 Box 12 code W should remain unchanged (as you comment suggests), how would this affect line 9 (employer contributions to HSA) on our 8889 forms?
