In the section on Quantum process tomography, Page 391, Chapter 8, Quantum Computation and Quantum Information by Nielsen and Chuang. it is given that
In general, $\chi$ will contain $d^4−d^2$ independent real parameters, because a general linear map of $d$ by $d$ complex matrices to $d$ by $d$ matrices is described by $d^4$ independent parameters, but there are $d^2$ additional constraints due to the fact that $\rho$ remains Hermitian with trace one; that is, the completeness relation $\sum_i E_i^\dagger E_i=I$ is satisfied, giving $d^2$ real constraints.
A post, Why does the $\chi$ matrix have $d^4-d^2$ independent parameters?, has been asked on this, which contains an answer by @DaftWullie, which make use of the Choi matrix,
where it seems like $\chi$ is used to represent the Choi matrix, not the $\chi$ matrix.
$\chi$ is a hermitian $d^2\times d^2$ matrix which must have $d^2$ diagonal real (independent) terms, and the number of terms below the diagonal is $\dfrac{(d^2-1)d^2}{2}$ that contains a total of $2\times\dfrac{(d^2-1)d^2}{2}=d^4-d^2$ of real terms. Therefore, the total number of independent real parameters considering only that $\chi$ is hermitian, is $(d^4-d^2)+d^2=d^4$.
The Choi matrix is given by, $\sigma=(I_R\otimes\mathcal{E})(|\alpha\rangle\langle\alpha |)$ where $|\alpha\rangle=\dfrac{1}{\sqrt{d}}\sum_i |i_R\rangle\otimes|i_Q\rangle$ is a maximally entangled state of the systems $R$ and $Q$.
$$ \sigma=(I_R\otimes\mathcal{E})(|\alpha\rangle\langle\alpha |)=\dfrac{1}{d}\sum_{i,j}|i_R\rangle\langle j_R|\otimes\mathcal{E}(|i_Q\rangle\langle j_Q|) $$ which can be interpreted as the block matrix with $\frac{1}{d}\mathcal{E}(|i_Q\rangle\langle j_Q|)$ as the $(i,j)^{th}$ block.
The $\chi$ matrix is defined by setting $E_i=\sum_m e_{im}\tilde{E}_m$, with $\{\tilde{E}_m\}$ being any orthonormal basis for the set of operators on the state space, such that $$ \mathcal{E}(\rho)=\sum_i E_i\rho E_i^\dagger=\sum_{m,n}\chi_{mn}\tilde{E}_m\rho\tilde{E}_n^\dagger $$ where the $(m,n)^{th}$ element of $\chi$ is $\chi_{mn}=\sum_i e_{im}e_{in}^*$ such that $$ \chi=\sum_{m,n}\chi_{mn}|m\rangle\langle n| $$ $$ \sigma=(I_R\otimes\mathcal{E})(|\alpha\rangle\langle\alpha |)=\sum_{m,n}\chi_{mn}(I\otimes \tilde{E}_m)|\alpha\rangle\langle\alpha |(I\otimes \tilde{E}_n^\dagger)=\sum_{m,n}\chi_{mn}|\tilde{E}_m\rangle\langle\tilde{E}_n| $$ where \begin{align}|\tilde{E}_m\rangle&=(I\otimes \tilde{E}_m)|\alpha\rangle\\ &=(I\otimes \tilde{E}_m)\dfrac{1}{\sqrt{d}}\sum_i |i_R\rangle\otimes|i_Q\rangle\\ &=\dfrac{1}{\sqrt{d}}\sum_i |i_R\rangle\otimes\tilde{E}_m|i_Q\rangle \end{align} and therefore $$ \chi_{mn}=\langle\tilde{E}_m|\sigma|\tilde{E}_n\rangle $$ Now, the Choi matrix can be written as, \begin{align} \sigma&=\sum_{m}(I\otimes {E}_m)(\dfrac{1}{d}\sum_{i,j}|i_R\rangle\langle j_R|\otimes|i_Q\rangle\langle j_Q|)(I\otimes {E}_m^\dagger)\\ &=\sum_{i,j}|i\rangle\langle j|\otimes\dfrac{1}{d}\sum_m{E}_m|i\rangle\langle j|{E}_m^\dagger\\ \end{align} Therefore, the $(i,j)^{th}$ block of the Choi matrix $\sigma$ is $\dfrac{1}{d}\sum_m{E}_m|i\rangle\langle j|{E}_m^\dagger$.
The $(k,l)^{th}$ term of the $(i,j)^{th}$ block of the Choi matrix is, $$ \sigma_{ij,kl}=\langle k|(\dfrac{1}{d}\sum_m{E}_m|i\rangle\langle j|{E}_m^\dagger)|l\rangle\\ =\dfrac{1}{d}\sum_m\langle k|{E}_m|i\rangle\langle j|{E}_m^\dagger|l\rangle\\ $$ $$ \sigma_{ij,kl}=\dfrac{1}{d}\sum_m\langle k|{E}_m|i\rangle\langle j|{E}_m^\dagger|l\rangle $$ We are free to choose $\tilde{E}_m=\sqrt{d}|t\rangle\langle q|$ such that $m=qd+t$ equates the Choi matrix and the $\chi$ matrix, therefore $$ \boxed{\chi_{ij,kl}=\dfrac{1}{d}\sum_m\langle k|{E}_m|i\rangle\langle j|{E}_m^\dagger|l\rangle} $$
Applying the trace preserving condition, $\sum_m E_m^\dagger E_m=I\implies\sum_m \langle k|E_m^\dagger E_m|i\rangle=\delta_{ik}$
This much is clear!
Then it says,
This directly influences the $\chi$: $$ \sum_j\chi_{ij,kj}=\delta_{ik} $$ There are (complex) constraints for all $d^2$ values of $i,k$. However, since everything is Hermitian, again this corresponds to $d^2$ real constraints. Thus, the total freedom remaining is $d^4-d^2$.
How do we obtain $\sum_j\chi_{ij,kj}=\delta_{ik}$ ?
How does imposing the trace-preserving condition $\sum_m E_m^\dagger E_m=I$ on the Choi matrix obtains the number of constraints on the $\chi$ matrix ?
My Attempt
Thanks @JSdJ for the hint.
$\chi_{mn}=\langle\tilde{E}_m|\sigma|\tilde{E}_n\rangle\implies \sigma=\sum_{m,n}\chi_{mn}|\tilde{E}_m\rangle\langle\tilde{E}_n|$
Therefore, in order for $\sigma=\chi$, we need $|\tilde{E}_m\rangle=|m\rangle$, where $m:0\to d^2-1$
$(I\otimes\tilde{E}_m)|\alpha\rangle=|\tilde{E}_m\rangle=\dfrac{1}{\sqrt{d}}\sum_i |i\rangle\otimes\tilde{E}_m|i\rangle=\dfrac{1}{\sqrt{d}}[|0\rangle\otimes\tilde{E}_m|0\rangle+|1\rangle\otimes\tilde{E}_m|1\rangle+\cdots+|d^2-1\rangle\otimes\tilde{E}_m|d^2-1\rangle]$
Let's consider the case when $d=2\implies d^2-1=3$,
Then,
where $\tilde{E}_m|i\rangle$ is the $i^{th}$ column of $\tilde{E}_m$, ie., $|i\rangle\otimes\tilde{E}_m|i\rangle$ is a column vector with the $i^{th}$ column of $\tilde{E}_m$ as it's $i^{th}$ block, all other elements are zero. So, $\sum_i |i\rangle\otimes\tilde{E}_m|i\rangle$ is the column vector with the columns of $\tilde{E}_m$ stacked on top of each other in order.
We can divide $|m\rangle$ into $d$ blocks of dimension $d$ such that let's take $m=qd+t$, where $q,t:0\to d-1$.
So, for $|\tilde{E}_m\rangle=|m\rangle$ we need to choose $\tilde{E}_m=\sqrt{d}|t\rangle\langle q|$, such that $\sigma=\sum_{m,n}\chi_{mn}|\tilde{E}_m\rangle\langle\tilde{E}_n|=\sum_{m,n}\chi_{mn}|m\rangle\langle n|=\chi$
$\therefore \chi_{ij,kl}=\dfrac{1}{d}\sum_m\langle k|{E}_m|i\rangle\langle j|{E}_m^\dagger|l\rangle$
Applying the trace preserving condition, $\sum_m E_m^\dagger E_m=I\implies\sum_m \langle k|E_m^\dagger E_m|i\rangle=\delta_{ik}$, how do we reach\begin{align} \sum_j\chi_{ij,kj}&=\delta_{ik} \end{align}