It appears that one way to obtain a desired example pair $G$ and $H$ is to let
$G$ be the disjoint union $G_1\cup G_2$ and $H$ be the disjoint union of
$H_1\cup H_2$, such that
- $G_1$ and $H_1$ have a common equitable partition, yet are not co-spectral; and
- $G_2$ and $H_2$ have the same number of walks of any length, yet they have no common equitable partition.
Clearly, the resulting graphs $G$ and $H$ will not be co-spectral and similarly won't have a common equitable partition. Nevertheless, the property of that $G_1$ and $H_1$, and $G_2$ and $H_2$, have the same number of walks of any length is preserved by the union.
To be more explicit:
For $G_1$ and $H_1$ one can take, e.g., $C_6$ (cycle of length $6$) and $2C_3$ (two disjoint triangles). These graphs are known not to be co-spectral and have a common equitable partition (see e.g., Fig. 3 in ).
For $G_2$ and $H_2$ one can just take the pair of co-spectral graphs with co-spectral
complements given in Fig. 4 in . That is, $G_2$ is $C_6\cup K_1$ (cycle of length $6$ with an additional isolated vertex) and $H_2$ is a star with one central vertex from which $3$ paths of length 2 start. Co-spectral graphs with co-spectral complements are known to have the same number of walks of any length (see Theorem 3 in ). Furthermore, since $G_2$ has an isolated vertex whereas
$H_2$ does not, they cannot have a common equitable partition (as their degree sequences must coincide.)
This results in graphs $G$ and $H$ consisting of 13 vertices. Perhaps smaller examples can be found.
 Fractional isomorphism of graphs, M. V.Ramanaa, E. R.Scheinerman and D. Ullman, Vol. 132, Issues 1–3, pp. 247-26, 1994. https://doi.org/10.1016/0012-365X(94)90241-0
 Enumeration of cospectral graphs, W. H. Haemers and E. Spence,
European Journal of Combinatorics, Vol. 5, Issue 2, pp. 199-211, 2004.
 Cospectral graphs and the generalized adjacency matrix, E.R. van Dam, W.H. Haemers and J.H. Koolen, Linear Algebra and its Applications, Vol. 423, pp. 33–41. 2007.https://doi.org/10.1016/j.laa.2006.07.017