Are you talking about the order of the .prj project files when you go to File >> Set Active Project or the order of the .c, .h, .fp, .uir files within a project?
You can change the order of the .prj files from the project window by selecting Edit >> Workspace >> Move Up (or Move Down). I haven't seen the order of these files change on its own.
You can change the order of the files listed in a project from the project window by selecting View >> Sort By (whatever). This order may change based on what Sort By you choose. E.g. Sort By Date will show the most recent at the top of the list. I don't know what No Sorting does.