You must run the DC_ERR_JAVA_SR_ORPHAN_V1 and the DC_ERR_JAVA_SRV2_UPDATE rules regularly to maintain your server.
These rules are stored in the DataChecker_rulefile.xml file that is the default rulefile of VPMDataChecker. This file contains all the rules.
The repair mode of the DC_ERR_JAVA_SR_ORPHAN_V1 rule can be launched only if the data model is Unified Typing. To enforce that rule the variable UnifiedTypingConfirmRepairSR must be set to Yes. If the variable is not set, the repair actions will not be done.
If you want to know more about the way to modify rule files, see Multi-Discipline Collaboration Platform: Data Administration Tools and Techniques: Using the Data Checker.