Given a matrix A of a strongly $k$ regular graph G(srg($n,k,\lambda,\mu$);$\lambda ,\mu >0;k>3$). The matrix A can be divided into 4 sub matrices based on adjacency of vertex $x \in G$. $A_x$ is the symmetric matrix of the graph $(G-x)$, where $C$ is the symmetric matrix of the graph created by vertices of $(G-x)$ which are not adjacent to $x$ and $D$ is the symmetric matrix of the graph created by vertices of $(G-x)$ which are adjacent to $x$.
$$ A_x = \left(\begin{array}{cccccc|ccc|c} 0&1&0&0&1&0&1&0&0&0\\ 1&0&1&0&0&0&0&1&0&0\\ 0&1&0&1&0&0&0&0&1&0\\ 0&0&1&0&0&1&1&0&0&0\\ 1&0&0&0&0&1&0&0&1&0\\ 0&0&0&1&1&0&0&1&0&0\\ \hline 1&0&0&1&0&0&0&0&0&1\\ 0&1&0&0&0&1&0&0&0&1\\ 0&0&1&0&1&0&0&0&0&1\\ \hline 0&0&0&0&0&0&1&1&1&0\\ \end{array}\right) = \left( \begin{array}{ccc} C & E & 0 \\ E^{T} & D & 1\\ 0 & 1 & 0\\ \end{array} \right) $$
It should be noted that
Interchanging/swapping any two rows (or columns) of $C$ does not affect matrix $D$ (and vice versa).
Any change in $C$ or $D$ or both $C$ and $D$ changes matrix $E$.
Problem: If some vertices of $G$ is rearranged (i.e., permuted), $A$ will be different, say, this new matrix is $B$. Again, matrix $B$ can be divided into 4 sub matrices based on adjacency of vertex $x \in G$ and $ B_x$ can be obtained.
Assume:
- $C$ is always the adjacency matrix of a regular graph and bigger than $D$.
- There exists an algorithm that always order $D$ (for a vertex $x \in G$) takes $O(K)$ time (assumed to be polynomial/exponential, does not matter).
Each row of E has different permutation, i.e., rows might have same number of 1's but different permutation/arrangement of 1.
For $n$ vertices there will be total $n$ numbers of $C,D$, each of them will take $O(K)$ (assumed to be polynomial) time to sort. If each $C$ takes time $O(f(n))$ to sort, then the total complexity will be $O(n \cdot K \cdot f(n))$.
Question: According to the three assumptions above, does there exist a polynomial time algorithm to sort $C$ so that $B=A$? I.e., is there a polynomial $f$ ?
The problem is connected to this question.
If anything is unclear, please ask a specific question, I will try my best to answer.
this will not be a direct answer at what does not really seem a direct question, which in its apparently big scope/ ambition pushes outside the bounds of SE questions but is nevertheless aimed to be a scientific and guiding response. you seem to be studying graph isomorphism in general, and as you are apparently aware the precise complexity of this is a major open problem. and it is known/ utilized generally that regular graphs are the "hard" ones for GI otherwise one can leverage nonuniform vertex degrees to (usually) significantly decrease the search space of vertex permutations.
so the best route to studying known hard scientific problems is to relate your own approach to the literature aka "terra cognita", which is quite large on this subject. for problems this significant, most straightforward approaches are attempted/ analyzed "somewhere". Here are some fairly close references to your technique, they share many close similarities. & then the task is to try to determine how your technique is different. Your basic idea of assigning columns/ rows of the adjacency matrix to different matrices is basically a partitioning algorithm of vertices into different sets. so:
complexity of open partitions / open question by McKay on mathoverflow. he asks about the complexity of partitioning regular graphs into vertex partitions with the "equitability" property that may be similar to yours. he is the writer of nauty the top software for graph isomorphism computations.
Efficient graph automorphism by vertex partitioning / Fowler et al. from abstract, an algorithm that runs in P time for all graphs tested including regular graphs.
My suggestion is also to try to convert your problem to isomorphism instances and empirically test nauty on it (just as the 1st paper uses empirical testing, which is accepted with conditions in this area), and that may be one of the more efficient known approaches, because nauty encodes vast swathes of state-of-the-art knowledge/ algorithm(s) on graph isomorphism complexity study.