"It would be conversion"

Then it should have gone through a Traditional IRA account first. This doesn't seem to be a rollover or a conversion. It seems your client cashed out retirement, then contributed to a Roth and has to meet those requirements for that tax year. You seem to have two separate activities:

1099-R = money Out.

5498 = money In, or she could have just kept it, since it is her money now.