Well, the PS wasn't mandatory, I think we understood that this could upset you. To be clear, reading your post, I started to see the problem coming at the point 4.
Duplicating a layout is duplicating a layout, and copy/past everything that is inside. It isn't cloning object types. Object types are common to your project, so if you add or remove a behavior on an object, it affects all instances of this object, no matter what layout it is in. Why ? Because it is common to use the same objects in different layouts. It is understandable when you look at the project window in C2, as the objects are not in a "layout directory", but in their own directory.
Event sheet from the first layout aren't used in the second layout, unless you include them, it's the object configuration that is common, and that is most likely what went wrong here.
There is nothing we can do here, it's too late, unless you kept a backup somewhere, or didn't close C2 for a while (Ctrl+Z is then your friend). Your problem wasn't duplication, but modification of used elements to fit your other layout.
EDIT/PS : seems DUTOIT and me understood you differently here. I hope your problem was the one DUTOIT understood ^^