Hi Neil,The message "Changes in this file have not yet been permanently saved" means that you hit the "view" button from the editor, and not the "save" or "save as" button. Even when they are permanently saved that way, they will be saved locally in the templates folder for that section. Those changes will immediately be seen by all students in that section, but not by students from other sections.
If it is in your server's OPL directory, you actually cannot edit it from a course's problem editor. You have to copy those edits into the OPL version from a command line.
If the problem set is instead pointing to a local copy of the problem in the course's template folder, then you would need to make the same edits to each course's template folder (which is why it can be nicer to use the OPL or to make your own Library like the OPL that is managed from the command line.)