The following VBA example creates a shape range, clones it, and fills the clone. The clone link is then restored.
Sub Test()
Dim s As Shape
Dim sr1 As ShapeRange
Dim sr2 As ShapeRange
Set s = ActiveLayer.CreateRectangle(2, 2, 4, 4)
s.Fill.ApplyUniformFill CreateRGBColor(255, 0, 0)
Set s = ActiveLayer.CreateRectangle2(1, 4, 5, 5)
s.Fill.ApplyUniformFill CreateRGBColor(0, 255, 0)
Set s = ActiveLayer.CreatePolygon(1, 2, 3, 4, 6)
Set sr = ActivePage.FindShapes(, cdrRectangleShape)
Set sr2 = sr.Clone
sr2.ApplyUniformFill CreateRGBColor(0, 0, 255)
sr2.RestoreCloneLink cdrCloneFill
End Sub