Updates: Status: NeedsDecision Comment #5 on issue 2677 by asmeu...@gmail.com: subs(Eq) does not work http://code.google.com/p/sympy/issues/detail?id=2677
When expr.subs(x**2, y) replaces x with sqrt(y), this is essentially assuming Eq(x**2, y), so I don't see any inconsistency here.
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