You can't (as far as I know) specify the axis. That would require exporting to Blender and flipping it, which is probably the route you should take so you have fine grain control. Is this a static mesh or is it animated?
If you go that route it's best to use UModel for your mesh exporting. I've run into a ton of bugs using batchexport, WOTgreal, etc.
So long, and thanks for all the fish