If you know what the gains are, you can enter them now instead of amending later. Create a substitute 1099-R with the total amount of the withdrawal in box 1, the taxable amount (attributable income) in box 2a, and use codes P and J in box 7.
Typically, most people would enter the Roth contribution, then be told by Turbotax that it is not eligible, and be recommended to remove it. However, the result of doing that is that nothing is reported on the tax return, so you don't have to follow those steps if you don't want to. Just leave the Roth off the return, and report the 1099-R now or later. (Roth contributions are not reported unless they are un-removed excess. There is nothing reported on the tax return that you made a Roth contribution if you later removed it within the deadline.)
The 5498 doesn't change because that's what happened in 2024. If the IRS actually tries to reconcile the records (and there is some evidence that they don't bother even though they make it seem like they do) then the 5498 will be offset by the 1099-R with codes P and J.
