After you did something with a selected area, you'll want to "deselect" it so that future operations apply to the entire canvas again.
To do this in Krita, click on Select -> Deselect on the menubar (keyboard shortcut: Ctrl+Shift+A).
Note: in some image editors, the keyboard shortcut is Ctrl+D instead. The reason "select nothing" is Ctrl+Shift+A is because "select all" is Ctrl+A.