"1099R shows total distributed, not the amount repaid."

Because the 1099-R is for money Out, and that is how much went Out; it's not their responsibility to Net it. What the taxpayer did with it is a different issue. There should be a 5498 to confirm they "put it back" which is a Rollover. It's just a Rollover. The Rollover treatment has been changed to allow for up to three years, as long as you are designating this is a qualified covid distribution.