(A(((BC)D)(EF)))
(A(((BC)D)(EF)))
(A((BD)(EF)))
(A((BD)(EF)))
(A(B(EF)))
(A(B(EF)))
(A(BE))
(A(BE))
(AB)
(AB)
A
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Could be the progression you require, otherwise as stated above you end up with (ABE).

If that is what you require, then this could be what you need, if not, it's a starting point ;)

s/\(([^)])[^)]\)/$1/
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