In the FAFSA if it imports the tax return information, it will count the rollover as income.
You then have to put the amount of the rollover in the field where it asks for it.
If you miss it, I don’t think you can do it later.
But you can ask the school to correct the FAFSA, not sure if FAFSA helpline can do it as well.
The school will probably want the 1099R showing that it was a rollover.