A combinatorial matrix reconstruction problem Given a positive integer $n$. For any symmetric $n\times n$ matrix $M$, write $M_{ik}$ for the $(i,k)$ entry, $M_k$ for the unordered list (multiset) of entries in row $k$, and $S(M)$ for the unordered list (multiset) of all pairs $(M_k,M_{kk})$.
(This is the corrected definition from July 22, 2022, after having read the discussion below.)
(i) For which $n$ does $S(M)$ determine $M$ up to a symmetric permutation (i.e., $P^TMP$ where $P$ is a permutation matrix)?
(ii) For the other $n$, what is the structure of the matrices $M$ that cannot be reconstructed up to a symmetric permutation?
 A: The meaning of the question is unclear due to the word "set". As Carlo proposed in a comment, I'll take it that we have an unordered list of $n$ unordered lists of $n$ elements, and we want to identify the symmetric matrices for which those $n$ lists correspond to the rows up to permutation.
Clearly this is possible for $n=1$. For $n\ge 2$, it is impossible in general, as indicated by this example (where $M$ is any symmetric matrix).
$$
   \pmatrix{0 & 1 & 0 \\
            1 & 0 & 0 \\
            0 & 0 & M} 
   \qquad
   \pmatrix{1 & 0 & 0 \\
            0 & 1 & 0 \\
            0 & 0 & M} 
$$
The two matrices are not equivalent under simultaneous row and column permutation since they have different diagonal elements.
Note that this counterexample works even if the rows are given as ordered lists.
Now let's consider the case that all the matrix entries are different, up to the constraints of symmetry. Now the equivalence class of the matrix can always be reconstructed. First, the diagonal entries are those appearing in only one row; place them in arbitrary order down the diagonal, say $d_1,\ldots,d_n$. Now the other entries can be identified: for $j\ne k$ the $(j,k)$ entry is the unique value that is both in the same row as $d_j$ and in the same row as $d_k$.
In the new formulation, diagonal elements are identified. This does not help for $n\ge 5$. Take two non-isomorphic simple graphs with the same degree sequence. The simplest example is a path of 4 edges, versus a triangle plus an isolated edge. These both give 2 of $\{\!\{ \mathbf{0},1,0,0,0\}\!\}$ and 3 of $\{\!\{ \mathbf{0},1,1,0,0\}\!\}$, where I wrote the diagonal element bold.
For larger sizes, use two non-isomorphic 2-regular graphs; for example , for $n=6$, a 6-cycle and two triangles both give 6 of $\{\!\{ \mathbf{0},1,1,0,0,0\}\!\}$.
