The issuer of that 1099-R is responsible for reporting money Out. They don't know what happened next.

You use the entry worksheet to indicate it was rolled over, and you put the amount rolled.

Agreed. Screen 13.1 "Rollovers" section

I assume this is for the 2024 tax year, meaning the original due date of the return was April 15, 2025.

So NOW gather the data to prove the rollover occurred with 60 days, since the IRS has no way to check it. Bank or brokerage accounts, Form 5498 from the receiving entity, et al.

Around 14-16 months later, by August through October 2026, the IRS will send the taxpayer a notice regarding the taxability of the distribution.

You will be ready to respond.