Denote $n$-by-$1$ vectors $(b_1, b_2, \ldots, b_n)^\top$ and $(1, 1, \ldots, 1)^\top$ by $b$ and $e$ respectively. By assumption, we have
\begin{align*}
e^\top b = 0, \quad b^\top b = 1. \tag{1}\label{1}
\end{align*}
Without loss of generality, assume $\sigma^2 = 1$. In addition, since both $Y$ and $S^2$ are invariant under the translation transformation, we can answer the question under the simplified condition $X_1, \ldots, X_n \text{ i.i.d. } \sim N(0, 1)$. In other words, $X := (X_1, \ldots, X_n)^\top \sim N_n(0, I_{(n)})$.
As a standard trick in multivariate analysis, write $S^2 = X^\top(I_{(n)} - n^{-1}ee^\top)X$, $Y = b^\top X$. It then follows that
\begin{align*}
S^2 - Y^2 = X^\top(I_{(n)} - n^{-1}ee^\top - bb^\top)X := X^\top P X.
\end{align*}
Due to the condition $\eqref{1}$, it is straightforward to verify that the matrix $P$ is symmetric and idempotent, whence
\begin{align*}
\operatorname{rank}(P) = \operatorname{tr}(P) = \operatorname{tr}(I_{(n)}) - n^{-1}\operatorname{tr}(ee^\top) - \operatorname{tr}(bb^\top) = n - 1 - 1 = n - 2.
\end{align*}
It thus follows by the distribution of multivariate normal quadratic form that $S^2 - Y^2 \sim \chi^2_{n - 2}$. On the other hand, clearly we have $Y = b^\top X \sim N(0, 1)$.
Last, let's show $Y$ and $S^2 - Y^2$ are independent, which is true if one can show $PX$ and $b^\top X$ are independent in view of $S^2 - Y^2 = X^\top P X = (PX)^\top(PX)$ is a function of $PX$. This can be further reduced to show $PX$ and $b^\top X$ are uncorrelated, because both of them are normally distributed as linear transformations of $X \sim N(0, I_{(n)})$. This is also straightforward to verify by $\eqref{1}$:
\begin{align*}
\operatorname{Cov}(PX, b^\top X) = PI_{(n)}b = (I_{(n)} - n^{-1}ee^\top - bb^\top)b = b - b = 0.
\end{align*}
In summary, for the joint distribution of $Y$ and $S^2 - Y^2$, we can "say" that
- $Y$ and $S^2 - Y^2$ are independent.
- The marginal distribution of $Y$ is $N(0, 1)$, the marginal distribution of $S^2 - Y^2$ is $\chi^2_{n - 2}$.