Run Clean Diagrams

When a user deletes an element (like a Screen in an SD), there might still be an AD file with a reference to that element (e.g. a Display Screen action).  If Creator just removed the information about the element from the SD file, then the AD would start to look like garbage because e.g., the name of the Screen would be gone forever.  So Creator just marks the elements as deleted and hides it from the SD editor.  After a lot of editing, these deleted elements may accumulate in the files, and they also take up disk space and memory

Path to access the option is: Project Explorer -> project name -> right click -> Clean diagrams.  This can only be done if there are no errors in the project.