The standard materialization will materialize rules and store the derived facts in the datamodel. It is not possible to update the materialization at a later point of time. The materialized rules are never again used for reasoning. This means that if you added facts to the knowledge base after materialization, OntoBroker was not able to detect that the materialized rules should be applied again. This means that when your knowledge base changes, you basically have to restart OntoBroker and materialize the rules again (this time with the new facts).
TIP: If you want to store the materialized facts in a file, just start OntoBroker with the -m option and execute the "exportAllModules" command. OntoBroker will dump all facts and rules of all ontologies of the knowledge base to multiple files.
TIP: You can use the new "-runscript" commandline option when starting the server to materialize a set of rules and store the resulting ontologies in a file. This allows you to materialize rules in a batch job.