Michael,
You can do this as follow:
1) Make a new Folder
2) Edit it, then Add all the relevant files in the other Folders into it by choosing Server in the filepicker and navigating to them and selecting them
3) Then use Download All in the new Folder
This works because those uploaded files are not actually "in" the Folders at all (as 1.9 course files were), but are really in Moodle's repository and referenced from the Folder. Using the Filepicker and going to Server, you can Add files to folders from other folders, from other activities and resources, and even from other courses as long as you have the permission to see them.
Now, having said that, depending on how many files you have, it may be as much work to do this as having the faculty download the zips from each folder, but it will give you one single zip to download and it lets you be selective as well (if you need.)