Do you have a copy of your 2016 return? if so, send them a copy of the return, the certified mail receipt showing that you submitted, and a detailed letter stating that you did submit. it wouldn't surprise me to know that it is probably warehoused somewhere but never got processed. Since it was mailed in, human error is probably the culprit.
Three weeks after you mail your amendment, you can start tracking its status at the IRS Where's My Amended Return? site or by calling their automated number 1-866-464-2050. Please note that it can take 12-16 weeks to process your amendment. Follow up with them constantly to make sure they receive the return.
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