Oh yes, flipping the screw blank end-over-end would be an awkward way to do it unless you wanted to make a screw with two starts each having opposite errors. Once the screws have gotten good enough you wouldn't need to bother with things like that.

I should have noted that it's a built in dividing head that turns the part between starts.

Any time you let go of a part you're going to have to re-locate it before you start cutting again, and you will lose accuracy in the process.