This message has to do with Linux/Unix more than with Airwave specific.
Unlike Windows, in Linux you can remove/delete directories and files when they are in use. This message basically tells you that the directory where your shell (Linux prompt) is in, is no longer at the same location. Airwave is installed in the directory: /root/svn; and during an upgrade this is renamed (moved) to /root/svn_old and a new /root/svn directory is created with all the files.
You 'bash' prompt remains in the same directory, so if you were in /root/svn before, after the upgrade it is still in the same location which is then named /root/svn_old and contains the old pre-upgrade data. So it might look that nothing has happened.
The message only appears if you were in a Airwave directory during the upgrade; and if you type just the command: 'cd' you will return to the home-directory.
So, harmless message, Linux related not somuch Airwave, and if you like to avoid it, before the upgrade run 'cd' to get to the /root homedirectory, then run: start_amp_upgrade -v <version_number>.