Where is this reference point; in the middle or in the corner? How is the original part drawing centered? For doing things like this, I usually set up a spoilboard with a couple of pins sticking up along the centerline which correspond to holes in my workpiece, outside the area that's being carved. The part drawing should be centered in the middle, not somewhere on the edge. Then when you flip the part over and set it back on the pins, you won't lose registration. From looking at your part, it's difficult to see how you're supporting it when you flip it over, but if it's not held down firmly, that would account for the malformation you're talking about.