After I finish editing my file and save it and then close the program when I reopen the program all my edits are gone. The file name has been changed with a "_01" at the end.
Are you sure you are saving a .MVP project? Sequential numbering sounds more like trying to export a finished film .MPG or .AVI etc) multiple times with the same file name. I'd check by doing a 'File' >> 'Save project as...' with a new name.