"not reported on form 1099-R?"

1099-R is for distributions. It is never netted against anything. It is not going to report a rollover. It's for money Out. They don't know what else was done with that money.

"the client received form 5498 showing the $50k as a rollover"

5498 is proof that a contribution or rollover or conversion was deposited into an account of a specific type and, if it applies, for a specific tax year. It's for money In. As long as you confirmed the info qualifies for an indirect rollover, then yes, it is reported.

But, we are missing amount details. If that distribution was from a Trad IRA, there would have been withholding deducted from the gross. You mention $50k, which makes it seem like this was a partial rollover of the taxpayer's net, not a rollover of gross including the tax makeup?

If the initial return didn't reflect the amount of the indirect rollover and that there is a rollover, then, if you don't amend it, the entire 1099-R wold be treated as taxable (subject to basis, of course).