If you're going to do what I think you are, it won't have any effect on the X-axis deflection. The pivot point (the rails), and the spindle/tool, will still be in the exact same positions relative to each other.

It will make a difference to the Z deflection, however I'm not convinced it will be that great. The Z-axis, although using unsupported rails, is quite a compact and stiff assembly. Although changing things around will reduce the pivot distance between tool and Z-rails, I wouldn't expect it to flex that much anyway. Certainly not much in relation to the flex of the X-axis.