I have an upper triangular system
$$ \begin{bmatrix} a_{00} & a_{01} & a_{02} & a_{03} \\ 0 & a_{11} & a_{12} & a_{13} \\ 0 & 0 & a_{22} & a_{23} \\ 0 & 0 & 0 & a_{33} \\ \end{bmatrix} \begin{bmatrix} x_0 \\ x_1 \\ x_2 \\ x_3 \end{bmatrix} = \begin{bmatrix} b_0 \\ b_1 \\ b_2 \\ b_3 \end{bmatrix}. $$
My goal is to remove $x_1$ from the system and just have
$$ \begin{bmatrix} a_{00}' & a_{01}' & a_{02}' \\ 0 & a_{11}' & a_{12}' \\ 0 & 0 & a_{22}' \\ \end{bmatrix} \begin{bmatrix} x_0 \\ x_2 \\ x_3 \end{bmatrix} = \begin{bmatrix} b_0' \\ b_1' \\ b_2' \\ \end{bmatrix}. $$
I think this is possible by reordering the states and then doing a QR factorization which would give something like the following from which the top row could be removed.
$$ \begin{bmatrix} a_0'' & a_1'' & a_2'' & a_3'' \\ 0 & a_{00}' & a_{01}' & a_{02}' \\ 0 & 0 & a_{11}' & a_{12}' \\ 0 & 0 & 0 & a_{22}' \\ \end{bmatrix} \begin{bmatrix} x_1 \\ x_0 \\ x_2 \\ x_3 \end{bmatrix} = \begin{bmatrix} b'' \\ b_0' \\ b_1' \\ b_2' \end{bmatrix} $$
I figured it out, I'll leave my method here to help others solve the problem in the future. Given a system $A \bar{x} = \bar{b}$
$$ \begin{bmatrix} a_{00} & a_{01} & a_{02} & a_{03} \\ 0 & a_{11} & a_{12} & a_{13} \\ 0 & 0 & a_{22} & a_{23} \\ 0 & 0 & 0 & a_{33} \\ \end{bmatrix} \begin{bmatrix} x_0 \\ x_1 \\ x_2 \\ x_3 \end{bmatrix} = \begin{bmatrix} b_0 \\ b_1 \\ b_2 \\ b_3 \end{bmatrix}, $$
first we'll reorder the state vector so the states to be dropped are at the beginning
$$ \begin{bmatrix} a_{01} & a_{00} & a_{02} & a_{03} \\ a_{11} & 0 & a_{12} & a_{13} \\ 0 & 0 & a_{22} & a_{23} \\ 0 & 0 & 0 & a_{33} \\ \end{bmatrix} \begin{bmatrix} x_1 \\ x_0 \\ x_2 \\ x_3 \end{bmatrix} = \begin{bmatrix} b_0 \\ b_1 \\ b_2 \\ b_3 \end{bmatrix}. $$
Call the above $A_\text{reorder} \bar{x}_\text{reorder} = \bar{b}$. Then take the QR factorization of the matrix
$$ QR = A_\text{reorder}, $$
and apply the rotation to $\bar{b}$
$$ \bar{b}'' = Q^T \bar{b}. $$
We now have a new upper triangular system $R \bar{x}_\text{reorder} = \bar{b}''$, and so we can just extract the bottom three equations
$$ \begin{align} A' &= R[2:4, 2:4], \\ \vec{b}' &= \bar{b}''[2:4]. \end{align} $$
This gives us our desired system
$$ \begin{bmatrix} a_{00}' & a_{01}' & a_{02}' \\ 0 & a_{11}' & a_{12}' \\ 0 & 0 & a_{22}' \\ \end{bmatrix} \begin{bmatrix} x_0 \\ x_2 \\ x_3 \end{bmatrix} = \begin{bmatrix} b_0' \\ b_1' \\ b_2' \\ \end{bmatrix}. $$
Simple example in python: