At FabLab AS220 in Providence, I gave a workshop on how to make wooden multicopter propellers with two-sided milling. The trick is to use a zero position in the middle of your files. Then you can do a separate 2D drilling job in order to make alignment holes all the way through your material and into the sacrificial layer. When you flip you material to work from the other side, you use wooden plugs through these holes in order to position your part accurately. See the pics for reference, follow this link to download the propeller STL files: