I am trying to reconcile a difference between two methods of finding $\mathbb{P}(|X|\geq y)$ for some RV $X$ and some $y > 0$.
Method 1
Consider the following line of reasoning: \begin{align*} &|X| \geq y\\ \iff& (X > 0\text{ and }X \geq y)\text{ or } (X < 0\text{ and } -X\geq y)\\ \iff& (X \geq y)\text{ or } (-X\geq y) &\text{since $y>0$}\\ \iff& (X \geq y) \text{ or } (X \leq -y) \end{align*}
Note that on the last line, the two events are disjoint. This leads us to believe $$ \mathbb{P}(|X| \geq y) = \mathbb{P}(X\geq y) + \mathbb{P}(X\leq -y) $$
Method 2
We have that $\{\{X > 0\}, \{X \leq 0\}\}$ is an event space. Then by the law of total probability, we have \begin{align*} \mathbb{P}(|X|\geq y) &= \mathbb{P}(|X|\geq y\:\vert\:X>0)\,\mathbb{P}(X>0) + \mathbb{P}(|X|\geq y\:\vert\:X\leq 0)\,\mathbb{P}(X\leq 0)\\ &= \mathbb{P}(X\geq y)\,\mathbb{P}(X > 0)+\mathbb{P}(-X\geq y)\,\mathbb{P}(X\leq 0)\\\\ \mathbb{P}(|X|\geq y)&= \mathbb{P}(X\geq y)\,\mathbb{P}(X>0)+\mathbb{P}(X\leq-y)\,\mathbb{P}(X\leq 0) \end{align*}
It seems that these two methods should always give the same answer, however they only coincide when further assumptions about the probabilities are made.
What is the resolution here?
You do not always have $\mathbb{P}(|X|\ge y | X > 0) = \mathbb{P}(X\ge y)$.
Instead, you have $\mathbb{P}(|X|\ge y | X > 0)\mathbb{P}(X > 0) = \mathbb{P}(X \ge y)$.
When you replace that in your formula (and similarly for the negative), you get exactly the same result as Method 1.