When starting a job, CM could warn the user if the file that is loaded has changed since it was loaded.
Since the ‘Save into other file’ functionality doesn’t work as expected (it behaves instead like a ‘Save As…’ command), I usually just resave into the same file as I adjust toolpaths, or enable/ disable paths for front and back cutting. If the file loaded has changed since it was loaded, then I forgot to reload it and will soon be sad since the wrong toolpaths will be running.