I would start by trying to reconcile the difference between the W-2 and the bank's records with the employer and the bank. The bank should have records of deposits that were credited; the employer should have records of the deposits. Does the difference represent deposits made by the employer in 2020? They would not show up on the 2019 W-2 but they will show up on the 2020 W-2.
Assuming that is the reason for the difference, you leave the W-2 alone. Report that you closed the account and withdrew the $140. Next year, if you don't change the situation, her W-2 will show $190 in contributions and you will again indicate you withdrew them all. You will get a 5498-SA statement of contributions in May, but it won't list the return, that will be listed on her 2020 5498-SA.
This is not an answer to your question, but there is something else you should know. "We" do not already have a family HSA. An HSA is an individual account owned by one person, like an IRA. You might own an HSA, your wife does not (for now). Second, if you are enrolled in an HSA-eligible family HDHP, then your spouse is considered also to be enrolled in an HDHP, even if she is not. As long as neither of you has disqualifying insurance, then both of you can make tax-deductible contributions to an HSA. The contribution limit on a family HSA is $7000 for 2019 and $7100 for 2020. This can be split between you in any way you want, as long as neither of you goes over the limit and as along as your combined total is not also over the limit.
So it is completely legal for you and your wife to contribute to separate HSAs, and the only reason to close your wife's account is if your account is fully funded. And if this money from your wife's employer is free from the employer (an employee benefit or cash match) why would you turn down free money? (For example, if her employer offers $500 of free HSA money each year, you should take the free money and reduce the contributions to your own account to $6500 or less.)
Unless you are fully funding your account, I would go to her employer, apologize for the confusion, and ask to reopen the account and make contributions, especially if they include free employer matching money. Adjust your own contributions down if needed. If you are not fully funded for 2019 and want the additional tax deduction, you can contribute out of pocket money to either HSA up until April 15 and count it as a 2019 deposit, as long as you inform the bank ahead of time that this is a 2019 deposit.
Unless there is some other reason you don't want your spouse to have assets in their name.
