The original question was which file to populate - the "original" or the "copy".

The 1040x Instruction states to use the "original".  But it should be noted that the "copy" file DOES NOT have the Form 9325 carried over to this file "copy".  The Form 9325 remains ONLY in the "original" file.

Why make a "copy" and the file DOES NOT have the Form 9325 is an open question but there must be a reason.  

The "copy" file is now your original filed copy without the Form 9325.  For your records does that make sense!