To clarify, are you asking about what to do if neither part can be found, or is it that you have found one side, but not the other?
If it is the second scenario and you have found one side but not the other, the solution is simple. Open the file in Pepakura Designer(possibly might work in Pepakura Viewer but I forget) and click the "2D Menu" tab at the top of the screen. In the third partition of the list there is an option labeled "Invert Pattern." Clicking this will reverse the 2D unfolded template. The 3D view will not change, but when you print and pep the unfolded parts they will form a mirrored partner to the original (if it was originally left, this will give you the right side, and vice versa). Generally speaking when armor parts are the same regardless of which side it's on, there's usually only one file for one side because it can be reversed for the other side by a few clicks of the mouse.
If you can't find either side, I don't know what to tell you. At least one side for any given piece should be in the database at this point (MissingSpartan7 always has a link in his signature, currently labeled "Reconstuction complete. Databases online").