With some trial and error, I seem to have figured out how to mix down my arrangement without having to flatten down the project.
I’m using Nuendo 4.3 on a Windows 7 system
It seems that the distance between the left and right locators has to be the exact length as the duration of your arranged project… for instance, if you have a, b, c and d in your arrangement track, the total playback time of all four is the duration of your arranged project.
Make sure you activate your arranger track, set your left locator to the left of your intro, and the right locator anywhere (to the right of left locator of course) as long as the distance between the right and the left locators is the same as the duration of your project after applying your arrangement.
Go to File > Export > Audio Mixdown and just export to the desired location… I hope this helps you out… all the best.