My enquiry was based on a test server so nothing terrible could have gone wrong in the worst case scenario. Even then we had backups. I understand that the upgrade from 1.9 to 2.0 changed the files dramatically but I am still curious about changes to the file system post Moodle 2.0. I constantly run test systems against the same file directory with all versions of Moodle from 2.4 to 2.8 without apparent harm. Being a test system that I mainly experiment with quizzing I don't actually write much to the file system, so my experience may not be representative.
I entirely agree with Petr that it would be a very bad idea to run different versions of Moodle against the same file system with live data but I would like to know if the upgrading of versions of Moodle after 2.0 does change the file system.