object duplication and export

hello im a begginer user of blender and i have encountered a problem where i try to edit an imported .obj file and then export it back to view it in another program.
i try to take the object duplicate it and turn it verticaly (on x axis) upside-down, so in blender it looks all good and nice but when i try to export it back and view it the original part still looks fine but the duplicate is all messed up and torn apart… a shapeless mess.

what might be the cause of this and how can i fix this… i dont feel like trying to make another one execly identical… that’ll take hours and wont be as good.

thanks in advance ^^

edit: here’s a pic to describe my problem… http://imageshack.us/photo/my-images/17/31368775.jpg/

Open it back in Blender, click the duplicate, and remove doubles (can be found in Tool shelf by clicking “T”). This may solve the problem.