The "Toggle structural view" is changing the visible models from LiteMol: Cartoon, Surface, Balls and Sticks corresponding to predefined types in web: Atoms, Surface, Cartoon
There are actually several issues:
Each binding site has its atoms, those atoms are not hidden but only coloured. Each pocket has3 items: pocket, pocket-atoms, pocket-res. The pocket is probably a subset of pocket-res used for connection between LiteMol and application. Seems like a solution is to hide/show not only the first one but all three of them.
Now only the colour disappear, but in some visualisation, the AA are still visible.