I’ve found the Linux zip file to be cumbersome for replacing a single file in a zip. The jar utility from the Java Development Kit may be easier. Consider the common task of updating WEB/web.xml in a JAR file (which is just a zip file):
jar -uf path/to/myapp.jar -C path/to/dir WEB-INF/web.xml
Here, path/to/dir is the path to a directory containing the WEB-INF directory (which in turn contains web.xml).