When you enter the online filing data, you create a facsimile copy of the 1099-R for data entry. The IRS does not want a copy of your paper 1099-R because they already received a copy of your 1099-R from your account administrator.
As long as what you entered matches what they have, they do not need your copy. If they want to see it, they will write you, so be sure to keep your original 1099-R in a safe place.
