Provided is a method and system for model transformation reapply. Through a programming model transformation, a target model is generated. The target model has one or more model elements. As manual changes are made to the target model, parts of the target model are marked as non-changeable by annotations. The annotations are inserted into respective model elements of the target model and indicate which parts are non-changeable and thus preservable. The annotations enable reapplying of the transformation to make changes to the target model but preserve manual changes made to the model elements based on the inserted annotations. The reapply of the transformation may be configured with options to handle the deltas between the existing target model and newly generated target models of the transformation.