I don’t think, that everything in root is deleted, because QSYS.LIB is in root as well and deleting all this would clean up your diskspace perfectly. So obviously you have problems with PASE and the associated progs and symbolic links. Try to reinstall PASE and QSHELL OS/400 options with GO LICPGM->Option 11 (Install Licensed Programs). If reinstall won’t work, try to deinstall the options first, then try a new install of these options. Hope this helps!