Let me rephrase your question in terms that would seem more natural to a model-theorist.
Fix a language $L$ and two expansions $L\subseteq L_1$ and $L\subseteq L_2$. Let $L_\cup = L_1\cup L_2$. Suppose $N$ is an $L_\cup$-structure, and $M$ is an $L_\cup$-substructure. Further, assume that in both reducts to $L_1$ and $L_2$, $M$ is an elementary substructure of $N$: $M|_{L_1}\preceq N|_{L_1}$ and $M|_{L_2}\preceq N|_{L_2}$. What can we say about the question of whether $M$ is an $L_\cup$-elementary substructure of $N$: $M\preceq N$?
This is a slight generalization of your question: You had a base language $L$ and expansions $L_1 = L\cup \{R_1\}$ and $L_2 = L\cup \{R_2\}$, i.e., each expansion just added a single new relation symbol. I think the general case of arbitrary expansions doesn't add much more complexity.
We certainly don't have $M\preceq N$ in general. Here is a very simple example: Let $L$ be the empty language, $L_1 = \{P\}$ and $L_2 = \{Q\}$, where $P$ and $Q$ are unary predicates. Let $M = \mathbb{N}$ and $N = \mathbb{N}\cup \{\infty\}$. In both structures, interpret $P$ as the set of even natural numbers and $Q$ as the set of odd natural numbers. Then $(M,P)\preceq (N,P)$, since the theory of a set with an infinite and coinfinite predicate has quantifier elimination. Similary, $(M,Q)\preceq (N,Q)$. But $(M,P,Q)$ and $(N,P,Q)$ disagree about the sentence $\exists x\, (\lnot P(x)\land \lnot Q(x))$.
It doesn't get much simpler than that: even with just unary predicates over the empty language, $M$ and $N$ can disagree about sentences with a single quantifier. So I don't think there's much to be said in the general case.
On the other hand, I can give you a positive answer under some very strong hypotheses on $M$. This actually comes from a paper (arXiv) I wrote with Chieu-Minh Tran and Erik Walsberg.
Using the same notation as above, we define an $L_\cup$-structure $M$ to be interpolative if it satisfies the following property: Whenever $X_1\subseteq M^n$ is an $L_1$-definable set and $X_2\subseteq M^n$ is an $L_2$-definable set, if $X_1\cap X_2 = \varnothing$, then there exists an $L$-definable set $Z$ such that $X_1\subseteq Z$ and $X_2\subseteq M^n\setminus Z$. That is, disjoint definable sets in the two expansions are separated by a definable set in the base language.
(Equivalently, replacing $X_2$ with its complement: whenever $X_1$ is an $L_1$-definable set and $X_2$ is an $L_2$-definable set and $X_1\subseteq X_2$, there is an $L$-definable set $Z$ with $X_1\subseteq Z\subseteq X_2$, i.e., an $L$-definable interpolant between $X_1$ and $X_2$. This justifies the name and makes the connection with the Craig interpolation theorem more clear.)
Let $T_1$ be an $L_1$-theory and $T_2$ and $L_2$-theory, such that $T_1$ and $T_2$ have the same set $T$ of $L$-consequences. Let $T_\cup = T_1\cup T_2$. We say the interpolative fusion $T_\cup^*$ exists if the class of interpolative models of $T_\cup$ is elementary.
Now if $T_\cup^*$ exists and $M$ and $N$ are models of $T_\cup^*$ (in particular, they are interpolative $L_\cup$-structures) and $M|_{L_1}\preceq N|_{L_1}$ and $M|_{L_2}\preceq N|_{L_2}$, then $M\preceq N$. See Theorem 2.7 in the linked paper.