Ideally, subject matter experts are empowered define things in a self service manner. Project managers know what the projects are called of course.
However, humans in a file browser will miss their target and make typos. People make mistakes. If these cause disruptions to the organization's operations, and stress to all involved, you might make a case for changing the procedure.
Discuss with users that you can improve their disappearing folders problem. Offer assistance and documentation for how to find moved folders. Come up with a short list of who really is responsible for maintaining these. Possibly there is an administrative process you can help automate, where at the same time a project in created in some other systems, a folder is created. By a script, or a least someone who takes care to put the tree how it should be.
File access control lists do not solve everything. NTFS allows removing delete subfolders and files, which also will prevent renames. However, this has additional possibly undesirable effects. The trick of the new folder in file explorer and renaming it will not work. Replacing the mystery of the moved folder, with New Folder that cannot be removed.
Fear of data loss can be overcome with a backup restore test. Do one to convince the IT side of the house that the recovery plan works.