I am sure there is ANT tags to do it but have used this 7zip hack in .bat script. I use http://www.7-zip.org/ command line tool. All the times I use this for changing jdbc url within j2ee context.xml file.
mkdir .\temp-install
c:\apps\commands\7za.exe x -y mywebapp.war META-INF/context.xml -otemp-install\mywebapp
..here I have small tool to replace text in xml file..
c:\apps\commands\7za.exe u -y -tzip mywebapp.war ./temp-install/mywebapp/*
rmdir /Q /S .\temp-install
You could extract entire .war file (its zip after all), delete files, replace files, add files, modify files and repackage to .war archive file. But changing one file in a large .war archive this might be best extracting specific file and then update original archive.