I managed to do that by a simple trick, add this line of code:
splitDockWidget(Dock1,Dock2,Qt::Horizontal);
before hiding Dock1, and this line:
splitDockWidget(Dock2,Dock1,Qt::Horizontal);
before hiding Dock2.
This fixed the problem of the arrangement of docked widgets, not sure if this is the best way but it works for me.