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Hi Josh, I was probably being unclear. My apologies.

This is not something that script can do. The architecture of OmniFocus is such that if you change the order of a set of focused projects, they will be pulled out of their containing folders.

If you would like OF to work in a different way, you can signal that to Omni through Help > Send Feedback ... in the main OF menu.

(The nearest I could think of is to generate a hyperlinked text/rtf version of the list which you can reorder to your heart's content, and still have links back into the OF database).