This is just a heads up, so you don't let yourself be confused about the instructions.
In the Coding Best Practices chapter there's a sub-chapter called Deleting a Table or Field from the Data Model. The specific instructions under 1.a and 1.b are internally instructions related to how Microsoft's works with their internal version control system.
The rest seems relevant enough; You need to rename the elements, pre-fixed with "DEL_". You need to apply the elements to the relevant "SysDeletedObects..." configuration key. You have to move the elements manually to your own "Upgrade" model.