2019 tax return wasn't filed after my wife received an ITIN

I'll answer some of your easier questions first. :)

There will be no penalty for you, because there is no tax due. The penalties are all based on how late you were in paying your tax bill, and because you are due a refund, there is no penalty. If you were to simply refuse to file your tax return in which you were due a refund, your only penalty would be forfeiting your refund.

When you file your 2020 tax return, the third stimulus payment does not factor into it at all. Only the first two stimulus payments, which were made in the year 2020, show up on the 2020 tax return. The third stimulus payment will come into play next year when you do your 2021 tax return.

Now, for the bigger questions:

First, you were correct to file your 2019 tax return to the Austin office, and you were also correct to assume that they would be filing your tax return when the ITIN was issued. However, take a look at this question from another user in 2013. The user describes a situation very similar to yours, in which he filed a tax return to Austin in order to get an ITIN for his wife, and Austin subsequently lost his return. Unfortunately, it happens. On the bright side, his story does have a happy ending; he did eventually get his tax refund.

The pandemic adds a further complication to your situation. The IRS is still facing a tremendous backlog in processing returns, although they claim that they are making progress. As of last week, they report that they "are processing tax returns dated as early as July 15, 2020." You sent your return last March, but you didn't receive your ITIN until November, so it is entirely possible that the IRS has not lost your return, but just hasn't gotten to it yet.

As to whether you should refile your tax return, that is a tough one. The IRS is currently saying, "We’re working hard to get through the backlog. Please don’t file a second tax return or contact the IRS about the status of your return." However, that is little consolation if you are really needing your tax refund.

If you are doing okay without your refund and stimulus payments, it is probably best to wait a while. The IRS will eventually get caught back up, and either they will process your return, or you will know that you need to resubmit it. You will eventually get the money that you are owed.

If you are in a situation where you need this money as fast as possible, you could resubmit your 2019 tax return. Include a letter with it explaining that you submitted it to the Austin office last year, you were issued an ITIN, and you have reason to believe that the original tax return was lost. Sadly, this may not actually get you your refund any sooner, but it might just make you feel a little better to take some action, and perhaps, if the original return actually is lost, it will result in positive action.