You should not try to file an amended return. The return that you are attempting to file will confuse the IRS and delay processing your return even more. Your 1099R has no taxable income so let the IRS fix your return for you. They have a copy of the 1099-R as well. You shouldn't try to file the amended return until after the original return has been completely processed. They will almost certainly recognize this error for what it is and adjust your return for you.
@coolbean
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