The Eclipse Clean command, Project -> Clean... on the menu bar, removes all OWL files from the OwlModels folder. Other cleaning effects include removing obsolete mappings from the mapping file (ont-policy.rdf) in the OwlModels folder, regenerating metrics files in the OwlModels folder, removing Prolog files from the OwlModels folder, recreating the reasoner-specific SadlBuiltinFunctions.sadl file in the ImplicitModel folder, and cleaning the Temp folder.
It is essential that the menu bar's Project dropdown menu has Build Automatically checked. If it is not checked no new OWL files and rule files will be created in the OwlModels folder in the course of doing a project clean. Of course Build Project can be initiated manually from the Project dropdown menu as an alternative.
Occasionally the state of the SADL IDE will become corrupted and behave in unexpected ways, including not running inference as expected. Doing a Clean/Build on the project will often resolve such problems.