I would setup the first print, then click "Save Toolpaths to Disk" to save the gcode and x3g files to your hard drive. Then make the change for the second print and do the same thing (just be sure to use a different file name).
Then you can compare the gcode files (since those are plain-text). Are the temperatures in the beginning of the gcode file different? There are plenty of free text file comparison tools that can also make this easy to compare if you don't know where to look.