TL:DR Here goes nothing. I never understood Form 5498-SA. I basically asked this question years ago and the reply I received was that Form 5498-SA is for information purposes only. So if that's the case, let me use this hypothetical example filing for tax year 2019:
Box 2 lists the total HSA contributions made in 2019
however note that the amount reported in Box 2 is for the calendar year (Jan. 1, 2019 - Dec. 31, 2019)
Box 3 lists the total HSA contributions made in 2020 for tax year 2019
I make my own contributions. My employer plays no part with the HSA. Now that info is out of the way,
Let's say Box 2 is $900
Let's say in Box 3 is $300
And of that $900 made in calendar year 2019, there was $500 applied to contributions in tax year 2018. Therefore I didn't report that $500 on the tax return for 2019. What I did report on my tax return is the difference of $900 - $500 = $400 plus the amount of $300 in Box 3. So the total deduction for contributions to the HSA reported on my 2019 tax return was $700.
Since the Trustee of my HSA submits this info to the IRS, they see my $700 deduction reported on Form 8889, and Form 5498-SA reports a sum total of Boxes 2 and 3 of $1,200 for contributions applied for 2019.
So if Form 5498-SA is for information purposes only, how does the IRS know I haven't broken rules? I could theoretically report an amount of on my tax return for contributions applied to 2019 that aren't even true (not that I would, I'm just saying). There isn't is another official IRS Form that I'm aware of which exists for 2019's tax return.
This happens every. single.tax.year.with contribution amounts reported on Form 5498-SA incorrect because Box 2 reports the contributions made for the entire calendar year regardless of the fact a portion of the total amount was applied to a previous tax year.
