Did you enter (or start to enter) a 1099-R in the W-2 section by mistake?

If you entered them in the correct place and the numbers are what are on the form then you will have no option but to mail in the return this year ... this is not your error however for some reason the EIN is not in the IRS system yet. 

I don’t understand. These 1099R’s are from Charles Schwab and Prudential. They have been same numbers for at least a few years and I confirmed that they are still in use. .?

Sometimes things happen ... have someone else confirm you have the numbers correct and if you do the paper filing will have to be done.