Ok good, this is the kind of feedback I needed.
Can you find an example link? Are they using the file-storage/file?file_id=12345 or the file-storage/view/folder/filename type links?
Only the second type of URL would change with the update I am proposing.
One solution is to create a symlink from the old folder name to the new folder name, so that regular web links will be resolved correctly, and the webdav urls will also work. The only client software that seems to have a problem with # is the various MS Web Folders variations.