To obtain changes in the schema from the database used to obtain the initial relational model data, the relational model data has to be refreshed. To do so, right-click in Project Explorer or Catalog Explorer the Relational Model Data storage container of the database you want to refresh and select Refresh Relational Model Data From a Database. Refreshing catalogs/schemas always happens per database.
This will start the Relational Model Data Retrieval Wizard, with just the database driver available which belongs to the Relational Model Data storage you right-clicked. Complete the wizard to obtain the relational model data. Any elements you uncheck will not show up in the new relational model data and will be considered 'removed'.
After the wizard has been completed, the designer will migrate the Abstract Entity Model to the new relational model data and modify the Abstract Entity Model according to the Project Properties and Designer Preferences set.
After the refresh process, the designer will present you a change log of all the actions taken.