After some botched attempts at formulating my question correctly, I stopped trying to simplify it and just ask straight out.
Here's the situation. We have a statement that we're trying to prove:
For all $x \in \mathcal X$, $A(x) \Rightarrow B(x)$.
We attempt to do this by contradiction. Define $\mathcal X' := \{x \in \mathcal X: A(x)\}$ and then we're equivalently trying to prove
For all $x \in \mathcal X'$, $B(x)$.
We assume the negation $\exists x \in \mathcal X':\neg B(x)$ and try to come up with a contradiction. Suppose we end up instead showing that
$\exists x \in \mathcal X':\neg B(x) \not \Rightarrow x \not \in \mathcal X'$
In other words, if there exists an $x \in \mathcal X$ such that $A(x)$, then $\neg B(x)$ doesn't imply that $\neg A(x)$. In other other words, we prove that $A(x)$ can not be contradicted by assuming $B(x)$. What does this say about $x$ such that $A(x)$? Can $B(x)$ ever hold if $A(x)$ holds and conversely, can $A(x)$ hold if $B(x)$ holds?
I would guess it simply means $A(x)$ and $B(x)$ are mutually exclusive, but I don't know. The quantifiers make everything kind of complicated.
Looking at your derived statement: $$\exists x \in \mathcal X':\neg B(x) \not \Rightarrow x \not \in \mathcal X'$$ Let's write explicitly the negations in this formula: $$\exists x \in \mathcal X':\neg(\neg B(x) \Rightarrow \neg x \in \mathcal X')$$ Now $\neg B\Rightarrow\neg A$ is equivalent to $A\Rightarrow B$, therefore the statement can be further rewritten as $$\exists x \in \mathcal X':\neg(x \in \mathcal X'\Rightarrow B(x))$$ Also, $\exists x:\neg P(x)$ is equivalent to $\neg\forall x: P(x)$ ("there exists an $x$ for which $P$ does not hold" is the same as "$P$ does not hold for all $x$"). Thus the statement can be further rewritten as $$\neg\forall x \in \mathcal X':x \in \mathcal X'\Rightarrow B(x)$$ Now obviously, for all $x\in\mathcal X'$, we have $x\in\mathcal X'$,therefore we can further simplify this to $$\neg\forall x\in\mathcal X':B(x)$$ But that is a direct contradiction to the assumption $$\forall x\in\mathcal X':B(x)$$