To patch single file in war (or jar) archive, first find the path of the file in archive:

jar tvf yourwar.war|grep yourfile.xml

Next, unpack it:

jar xf yourwar.war path/to/yourfile.xml

Make your changes and add file into .war file w/following command (execute in same directory where you unpacked it):

jar uf yourwar.war path/to/yourfile.xml

Done!