First, box 2 on the 5498-SA often does not match the code W amount in box 12 on the W-2. So the IRS will not flag two different numbers as a problem.
The code W amount on box 12 on your W-2 includes what your employer contributed in 2019 PLUS what you contributed through payroll deduction in 2019.
Box 2 on the 5498-SA is
1. the sum of all contributions made in 2019 (both Code W and direct contributions)
2. any contributions that you made in 2019 for 2018
3. also includes any trustee to trustee transfers from an IRA to the HSA.
4. however, any excess contributions for 2019 are not included in Box 2.
So you can't compare the two without knowing if the other items come into play.
You should ask your employer for each year for which you have a question if they included the employer contribution AND your contributions made by payroll deduction in the amount with W in box 12 on your W-2.
If the employer did not do this, then you need to ask for a corrected W-2.
If you have not yet e-filed your 2019 return, you have time to update your tax return. Note that there is no advantage to e-filing your return before January 27th (this year) because the IRS won't open e-filing until that date (except for some returns taken as tests). Once you submit for e-file, you can't fix anything on your return, and you would have to amend your return - a hassle when you could have just waited and fixed your return before e-filing.
As for 2018, if the code W amount did not include the employer contribution, then you should get a corrected W-2 and amend your 2018 return. Unfortunately, you can no longer withdraw excess contributions for 2018 (I think I spoke about this in another post with you), but it would get your 8889 and 5329 forms to match what they should be.
I am a bit concerned at this point that your accountant previously reported your contributions based on the 5498-SA. Was he/she aware that the box 2 amount may not be the code W amount? TurboTax uses the code W amount to determine your HSA contribution (plus whatever you contributed directly to the HSA outside your employer).
At this point, because I cannot see your tax returns, I am concerned there perhaps you didn't even have an excess contribution in 2018, or that your employer incorrectly reported your Social Security and Medicare taxes (the code W amount should have been removed from Wages in boxes 1, 3, and 5 of your W-2, so SS and Medicare taxes should be less).
What you might do is get the corrected W-2s and perhaps consult with a different local tax pro who has a lot of experience with HSAs.
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