I'm sure there's a way to do it, but why would u want to? I guess if your TV or projector cannot decode over-under I understand, but over-under is already halving the resolution once, slicing the resolution in half the other way on top of that would likely result in a pretty ugly picture compared to the original.
How do I convert over-under 3D content to Side-by-side 3D ?
I'm not aware of a product that does this, but I've not ever looked closely.
Unless it's your only option, you wouldn't want to do this. Side by side and over/under both drop half the resolution either horizontally (Side by side) or vertically (over under). If you would convert from one to the other, you would lose yet another 1/2 resolution, resulting in 1/4 resolution of the original.