I personally like to just create the whole JAR file all over again. It is very simple, and I don't have to worry about all the different possible codes for jars...I just use the standard "jar cmf nameofmf.mf nameofjar.jar *.class *.otherfiles". Here are some links to help you with JAR files (and specifically what you are asking for). If you create the jar again, it will delete your old one, so you don't have to worry about updating or what not.
These are links which I found hours finding...Add them to your bookmarks and they you will be doing yourself a favor.
“Don’t worry if it doesn’t work right. If everything did, you’d be out of a job.” (Mosher's Law of Software Engineering)
“If debugging is the process of removing bugs, then programming must be the process of putting them in.” (Edsger Dijkstra)