Just keep the 1099S with the tax records as it does not get reported on the tax return.
Anything that takes place within the retirement account does not impact the return. If IRS does ask, you will simply let them know that this was inside the IRA and does not go on the individual return.
However, the issuer of the 1099-S should have requested the EIN for the IRA and used that on the 1099-S.
Here's more info on Sale of IRA Property.
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