"My problem is that I know the IRS has a 1099-R showing a total distribution that is taxable"

Only until you file the tax form to follow up with what happened next. The 1099-R is only the first step and the issuer doesn't necessarily have the info for what happened to those funds. The 5498 then is issued and is meaningful as the next step which reflects what was done, if anything, and for how much of the money, and where.

You stated "rollover" and if that was not Direct, then that's why the first entity issues 1099-R for the distribution coded as such. Even if the entire account was closed, that doesn't make the distribution taxable, if something is then done that makes it not taxable, such as Rollover within the timeframe to a similarly deferred and qualified account.

It seems maybe your client did not take possession of the funds in between, because you do not mention a required withholding that would need to be made up in the gross redeposit to the new account, from the distribution. That is always a consideration = partially taxable due to not making up the missing portion while executing a rollover manually by the taxpayer.