If a button for a toolbar is hidden in the tutorial, then the corresponding toolbar should be closed.
If anything, perhaps there should be a way to disable dialogs (toolbars are dialogs as well), so they are closed and can't be called. Then, you could automatically disable any toolbar buttons that call disabled dialogs, same as other menu buttons.
Otherwise, it can get pretty messy (several buttons could call the same dialog, does hiding some of them close the dialog? Does hiding an entire toolbar close all dialogs that can be called with that toolbar? Does it matter if buttons are invisible? Can invisible buttons be hidden to disable their shortcuts? ...) and it's probably easier for Yona to just manually add closing instructions where buttons for dialogs are hidden to also close them if open.
As Leartin said, this could be next to impossible. Maybe closing all but scenario window for each chapter would be a much easier solution.