If you have merely hidden atoms - for example, by using the Zapper tool, or any of the Selection > Hide commands, then you can easily make these atoms visible again by using the Selection > Show All command.

If you want to keep some atoms hidden, use the Site Browser (Window > Sidebar > Site Browser). The Site Browser contains checkboxes for atom and element visibility ("Vis").

If you are in "Molecule Mode" and have actually deleted some atoms, then use the Undo command to restore the deleted atoms. You may wish to peruse the History pane of the Overview window, in order to locate the most approriate "undo" state.