It is possible to edit a .sfx file by using a script. .sfx files are zipped XML files, so you would unzip the .sfx file, edit the resulting XML, and zip the result back up.
More likely you want to use a script to edit a model and save the model as sfx file. Many aspects of models can be altered by using set_param and related commands; https://www.mathworks.com/help/simulink/configuration-sets.html?s_tid=CRUX_lftnav
