The FileSave (or may be all verbs) works with GUI, but not without.
If you use without -z (same as --without-gui) that will save the change.
inkscape-svn -z --select=bola --select=rect --verb=SelectionDiff --verb=FileSave --verb=FileQuit desenho.svg; inkscape-svn desenho.svg
The problem will occur with "inkscape --shell" too.
I'm using inkscape from svn rev21113
The FileSave (or may be all verbs) works with GUI, but not without.
If you use without -z (same as --without-gui) that will save the change. SelectionDiff --verb=FileSave --verb=FileQuit desenho.svg; inkscape-svn desenho.svg
inkscape-svn -z --select=bola --select=rect --verb=
The problem will occur with "inkscape --shell" too.