@BobKamman thanks again really appreciate.

Whatever I mentioned on my last post if it is correct please let me know;

My question is what should I do for 1040 which is incorrect. You meant first file 1040-NR F1 visa and on the top mentioning " "Amended from 1040" and attach 1040 (incorrect one) along with making a 1040-X for incorrect one and explain what the client should pay as a non-resident: The client has completed the 1040-NR form and should pay an amount of A dollars, since client had previously received a refund of B dollars in error through Form 1040, now required to pay a total amount of C dollars.

In addition for page 1 of 1040-X for 1040(incorrect one) and page 2 , part 1; should not enter any information, just fill out part II that what happened and 

In fact I file just one 1040-X for incorrect one. if I did not understand, please correct me!