I know that by using Jordan-Wigner transform(JWT), we can transform spin-$1/2$ systems into fermions. My problem is, for example, after JWT, we have a hamiltonian of form $$\epsilon\left(c_{1}^{\dagger} c_{1}+c_{2}^{\dagger} c_{2}\right)+\lambda\left(c_{1}^{\dagger} c_{2}^{\dagger}+c_{2} c_{1}\right)\tag{1}$$ with $\lambda$ and $\epsilon\in \mathbb R$. If I directly write it as quadratic form $$\left( \begin{matrix} c_{1}^{\dagger}& c_2& c_{2}^{\dagger}& c_1\\ \end{matrix} \right) \left( \begin{matrix} \epsilon& \lambda& 0& 0\\ \lambda& 0& 0& 0\\ 0& 0& \epsilon& 0\\ 0& 0& 0& 0\\ \end{matrix} \right) \left( \begin{array}{c} c_1\\ c_{2}^{\dagger}\\ c_2\\ c_{1}^{\dagger}\\ \end{array} \right) $$ the eigenvalues of the middle hermitian matrix will be $$0,\epsilon ,\frac{\epsilon \pm \sqrt{\epsilon ^2+4\lambda ^2}}{2}$$
But if I change eq.(1) into another form with canonical commutation relation for fermions as follows: $$ \begin{align} &\epsilon \left( c_{1}^{\dagger}c_1+c_{2}^{\dagger}c_2 \right) +\lambda \left( c_{1}^{\dagger}c_{2}^{\dagger}+c_2c_1 \right) \\ &=\epsilon \left( c_{1}^{\dagger}c_1+c_{2}^{\dagger}c_2 \right) +\frac{\lambda}{2}\left( c_{1}^{\dagger}c_{2}^{\dagger}+c_2c_1 \right) -\frac{\lambda}{2}\left( c_{2}^{\dagger}c_{1}^{\dagger}+c_1c_2 \right) \\ &=\frac{\epsilon}{2}\left( c_{1}^{\dagger}c_1+c_{2}^{\dagger}c_2 \right) +\frac{\epsilon}{2}\left[ \left( 1-c_1c_{1}^{\dagger} \right) +\left( 1-c_2c_{2}^{\dagger} \right) \right] +\frac{\lambda}{2}\left( c_{1}^{\dagger}c_{2}^{\dagger}+c_2c_1 \right) -\frac{\lambda}{2}\left( c_{2}^{\dagger}c_{1}^{\dagger}+c_1c_2 \right) \\ &=\frac{\epsilon}{2}\left( c_{1}^{\dagger}c_1+c_{2}^{\dagger}c_2 \right) -\frac{\epsilon}{2}\left[ c_1c_{1}^{\dagger}+c_2c_{2}^{\dagger} \right] +\frac{\lambda}{2}\left( c_{1}^{\dagger}c_{2}^{\dagger}+c_2c_1 \right) -\frac{\lambda}{2}\left( c_{2}^{\dagger}c_{1}^{\dagger}+c_1c_2 \right) +\epsilon \end{align} $$
The same reason, we can write it as quadratic form $$\mathcal{H}=\frac{1}{2}\left(\begin{array}{cccc} c_{1}^{\dagger} & c_{2} & c_{2}^{\dagger} & c_{1} \end{array}\right)\left(\begin{array}{cccc} \epsilon & \lambda & 0 & 0 \\ \lambda & -\epsilon & 0 & 0 \\ 0 & 0 & \epsilon & -\lambda \\ 0 & 0 & -\lambda & -\epsilon \end{array}\right)\left(\begin{array}{c} c_{1} \\ c_{2}^{\dagger} \\ c_{2} \\ c_{1}^{\dagger} \end{array}\right)+\epsilon$$
But this time, eigenvalues become $$\pm \sqrt{\epsilon ^2+\lambda ^2}$$
I think this might be the reason that the unitary used to diagonalize the middle hermitian matrix cannot keep the canonical commutation relation for fermions.
So my problem is, after JWT, is there some routine that we can write the right hermitian matrix so the eigenvalue of the hermitian matrix is the answer we want?