Whenever notes have been selected for a particular clef, a badge appears on the clef showing the total number of notes selected in that staff.
For any given staff, there might be selected notes that aren't currently visible on the screen.
To be sure you are clearing (de-selecting) all the notes for a clef...
- Tap the green clef badge showing the number of notes currently selected.
- After it turns into a red X, tap it again to clear all of the notes in that staff.