You can delete a JAR file from the database but retain its classes as classes no longer associated with a JAR. Use remove java with the retain classes option if, for example, you want to rearrange the contents of several retained JARs.
For example, from isql enter:
remove java jar 'utilityClasses' retain classes
Once the classes are disassociated from their JARs, you can associate them with new JARs using installjava with the new keyword.