When you compare and merge two files, PDF Merge creates a temporary merge file and opens it in Adobe Acrobat.
By default, the merge file includes any objects that are the same in both the original PDF file and the revised PDF file, as well as any objects that are unique to the revised PDF file.
A unique object is an object that exists in one file only, or that exists in both files but has changed between the two files—for example, the object's position, color, font, or stroke thickness has changed. If an object exists in both files but has changed, PDF Merge retains the version of the object from the revised file and discards the object from the original file.