I used the following command:
java -jar bfg-1.13.0.jar --delete-files "settings.xml"
And the settings.xml file was correctly removed from the master branch. The file is deleted and is even omitted when looking at old commits, which is just what I wanted.
However, if I look in other branches, I still see the settings.xml there. I thought maybe I needed to merge the master branch into these others branches, so I did that, but the file still exists in those other branches.
Does anyone know why only the master branch was cleaned?