I am in the process of figuring out what to withdraw for a newly discovered over contribution form 2018 and 2019. This all came to light when I was trying to solve a mis-contribution for 2020 (i am no longer eligible but my employer still directly deposited to my HSA this year). When reviewing my taxes from 2018, I realize by W2 HSA contribution does not match my 5498 form. My accountant reported by over contribution in my 2018 taxes based on my 5498 form. I have yet to get my 5498 form from my HSA for 2019, but from my calculation, my W2 will not match it. It appears my employer reports only the employee contribution and not the employer contribution with it. My 5498 form obviously captures both my employee and employer contribution. When I withdraw my over contribution, I am basing it off of my 5498 form. Will the IRS flag if there is no match between my W2 and what I take out via excess contribution? I just want to take care of all these over contributions/miscontributions so it does not carry over.
