Here's an idea that might have some promise if it is possible.
The idea stems from creating almost a "master folder" of information, but rather copy the folder to courses again and again, like it is now, and then have to delete the duplicated created in each course...maybe folders can be 'linked' or 'synced' in a way (if you want) to the master folder or sub-folder.
The reasoning behind this is because I teach 5 sections under 1 course. When I add something to the resource library, let's say in a folder with new notes or additional notes that I create on the fly, I now need to re-copy the folder to each course to show the added item, and then delete the duplicated folder that was already shared so the students do not get confused.
Might be a long shot, but it does increase workflow and create a more seamless way to update contents of folders in multiple courses and also provide an avenue to control information so each class has exactly the same information if need be.