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"but she has a 1099 R showing it's taxable."
Because a 1099-R is the money Out. All they knew was, she took out funds. They have it as taxable, because they don't know about any condition for what she did, afterwards.
"She also has a 5498 showing the rollover."
The 5498 is for money In. As long as you confirmed this meets the requirements as a nontaxable distribution due to timeliness and account type for the deposit and that is the Gross distribution, you continue on with your entry, regardless of the 1099-R.
"So it's correct to input this in Lacerte with a code of G??"
If that 1099-R has a G, you input the G. If it has something else, you input that something else. You are not preparing the 1099-R; you are referencing it.
"Or is there another way to back it out somewhere else?"
"Level Up" is a gaming function, not a real life function.
