Where is their project stored? This sounds like what usually happens when there's a file access conflict in which an external program uses/locks the project files while you're working on them, leading to GM being unable to write to them and, therefore, while keeping the changed contents in memory, they won't be reflected in the file and thus can't be re-loaded when the project or individual files of it are closed and then re-opened. Common causes for this are cloud drive sync services, so if your student stores their project in something like a Dropbox or OneDrive folder, they'll have to take it out of there.