For a lot of armor permutations, when one piece is simply a miror image of the other, only way file was included in the .Zip to save on space, because there are some simple, straight forward methods for getting a mirror flipped product out of the same file.
One way to do it is to look in the "Other" section in version 3 of Pepakura designer and toggle the option of "Mirror Invertion." You may notice that the 3d preview doesn't flip. This is normal. Nothing has gone wrong. The 3d preview is just a reference, not the final development. The "2d pattern" window is what will print what you see. When you do this, you can just do your folds the same for both builds.
The other option is to do the opposite of what you did the first time. I will try to explain this. So, in Pepakura there will be two kinds of lines, a dashed line and a line with dots and dashes. When you go to fold the paper, or the foam, based on those lines, you always pick one for "Mountain Folds" where you fold down along the line to make "mountains," and on the other type of line you fold up to make "valleys." So you go through the build using the dashed lines as mountains and the dotted lines as valleys. Then, you reprint all the pieces but this time, you do the opposite, dashed lines are valleys and dotted lines are mountains. Doing this means you will have now created a mirror image of the pieces because you have folded everything the opposite way.