the IRS does not want a second return.   I understand the issue is that with paper filing, unless you used a method where yoU got proof of delivery, there's no way to know if the IRS got your return unless or until it shows up in where's my refund. 

your best option is to call because submitting a second return can actually delay the refund assuming the IRS hasn't already mailed the check but you never got it. 

800-829-1040

First choose your language.
Then 2
Then 1
Then 3
Then 2
When asked for SSN do nothing it will ask twice
Then 2
Then 4
You should then be transferred to an agent, but there is likely to be a long wait.

there is also the Tax Advocate Service.   

first you should try multiple times to contact the IRS through the method above otherwise the TAS may just tell you the same thing  - contact the IRS directly.

"Last year, we assessed where our efforts have the greatest impact, and identified four
types of issues in which the IRS seemed to get the right answer (though slowly). Those
cases involve the processing of original tax returns, amended returns, rejected and
unpostable returns, and injured (but not innocent) spouse claims. We determined that
TAS generally won’t accept cases involving these pure processing issues so we could
focus on higher-impact problems."

https://taxpayeradvocate.irs.gov/about-us/learn-more-eligibility

https://taxpayeradvocate.irs.gov/Media/Default/Documents/TAS_change_case_criteria_6_12_12.pdf