The reason is an incorrect listener. Testing instructions: 1. Open / create a FileProject with any logical component with an empty presence condition (empty by default). 2. Save the project if it is still marked dirty 3. De-select and select the component again 4. Observe: The model is NOT marked dirty (i.e. is not changed) 5. Add any presence condition to the component 6. Save 6. Observe: A presence condition can be added 7. Repeat the steps 2 to 4 8. Remove the presence condition from the component 9. Observe: The presence condition can indeed be removed.