To delete an existing certificate, use keytool -delete command, for example: 
keytool -delete 
-alias keyAlias 
-keystore keystore_name 
-storepass password
 
For a complete list of possible options for the -delete command, refer to the keytool documentation at:
http://java.sun.com/j2se/1.4.2/docs/tooldocs/solaris/keytool.html
 See also: