Let $A,B$ be finite SI-algebras and $V(A)$ be congruence-distributive. Then $V(A) = V(B) \iff A \simeq B$
$"\Rightarrow"$ Assume that $V(A) = V(B)$. By a corollary by Jónsson, all the SI-algebras from $V(A)$ are in $HS(A)$. and $V(A) = IP_S(HS(A))$. By the assumption we have $ V(A) = IP_S(HS(A))= IP_S(HS(B))$ $ = V(B)$. Now, a variety is generated by the SI-algebras within it. I am lost how to use it from here to get the desired result.
$"\Leftarrow"$ Assume that $A \simeq B$. Then $\forall C \le A, \exists D \le B$ such that $C \simeq D.$ And, for all $n\in \mathbb{N}$, $A^n \simeq B^n$. Finally $\forall A_H \in H(A), \exists B_H \in H(B)$ such that $A_H \simeq B_H$. Hence, up to isomorphism every algebra in $V(A)$ is similar to some algebra of $V(B)$, and vice versa. Thus, $V(A) = V(B)$. This direction seems like it is relatively trivial when considering that $V(A) = HSP(A)$.