What should I do when the recommender is not replying?
I would do a couple of things.
First, see if you can quickly organize a different recommender. Maybe futile, but it might work. Long term it might be useful to have a backup in any case.
Second, but simultaneously, inform the university to which you are applying that you can't reach the recommender and that Covid may be the reason. Tell them you have a copy of another letter from this person and ask for their advice on how to proceed. Give the name and email of your recommender, I think.
I suspect that people will be reasonable, given the general disruption. It shouldn't reflect badly on you if you do due diligence in getting recommendations. They may even be a bit &quot;soft&quot; about deadlines for such things. Note that admissions to doctoral programs is normally handled by people, not machines, and the people are all facing various kinds of disruption.
Finally, note that you not getting feedback from the recommender doesn't necessarily mean that they aren't otherwise doing their part. There may be a lot of reasons for not replying, many of them valid.