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I might be misunderstanding the nature of the question. It seems you want to work with subscripted variables in a situation where some subscript parts denote independent variables? If so, I would suggest separating into two steps. (1) Use code...
Mathematica 10.3 gets it wrong with this calculation (A \[Intersection] B) \[Union] (A \[Intersection] C) It seems to work if we inactivate Union and Intersection: Inactivate[ replRule := {HoldPattern[ x \[Element] ...