After you file

if you are amending ,

although not strictly correct, you can change the 1040X line 18 Overpayment  to  -0-

 

In Part III you can state you never got your original refund.

OR

 

go here to start a refund trace.

https://www.irs.gov/faqs/irs-procedures/refund-inquiries/refund-inquiries-0