From Rotman's Algebraic Topology:
Assume that $X = X_1^{\circ} \cup X_2^{\circ}$ and $Y = Y_1^{\circ} \cup Y_2^{\circ}$; assume further that $f : X \rightarrow Y$ is continuous with $f(X_i) \subset Y_i$ for $i=1,2$. Then $f^R_* D = D' f_*$, where:
$f_* : H_n(X) \rightarrow H_n(Y)$, and $f^R_* : H_{n-1}(X_1 \cap X_2) \rightarrow H_{n-1}(Y_1 \cap Y_2) $ is the restriction of $f$ and $D, D'$ are connecting homomorphisms of Mayer-Vietoris sequences.
$D$ is defined as $D = dh^{-1}_*q_*$, where $d$ is a connecting homomorphism of the pair $(X_1, X_1 \cap X_2)$, and $h$ and $q$ are inclusions defined by $h : (X_1, X_1 \cap X_2) \rightarrow (X, X_2)$ and $q : (X, \emptyset) \rightarrow (X, X_2)$.
I started by using the two short exact sequences $0 \rightarrow S_*(X_1 \cap X_2) \xrightarrow i S_*(X_1) \oplus S_*(X_2) \xrightarrow p S_*(X) \rightarrow 0 $ and $0 \rightarrow S_*(Y_1 \cap Y_2) \xrightarrow i S_*(Y_1) \oplus S_*(Y_2) \xrightarrow p S_*(Y) \rightarrow 0 $ that are connected by the induced maps from $f : X \rightarrow Y$. We then have a commutative diagram with exact rows :
$\dots \rightarrow H_n(X_1 \cap X_2) \xrightarrow {i_*} H_n(X_1) \oplus H_n(X_2) \xrightarrow {p_*} H_n(X) \xrightarrow \delta H_{n-1}(X_1 \cap X_2) \rightarrow \dots$
$\dots \rightarrow H_n(Y_1 \cap Y_2) \xrightarrow {i'_*} H_n(Y_1) \oplus H_n(Y_2) \xrightarrow {p'_*} H_n(Y) \xrightarrow \delta' H_{n-1}(Y_1 \cap Y_2) \rightarrow \dots$
connected again with induced maps from $f$, where $\delta$ is a connecting homomorpism.
I can see that $\delta' f = f^R \delta$, but I'm not sure how I'd use this to show $f_*^RD = D' f_*$.
Any hints or suggestions?
We know that $D = dh^{-1}_*q_*$ and $D' = d_*'h'^{-1}_*q'_*$. If I can show that that $f_*$ commutes with each $d_*$, $h_*$ and $q_*$, then we will be done.
$q_*$ is induced by inclusion $(X, \varnothing) \hookrightarrow (X, X_2)$ and $q_*'$ by $(Y, \varnothing) \hookrightarrow (Y, Y_2)$. Since, $f(X_i) \subset Y_i$, $f$ induces map at the relative chain level: $ f_\# : C_*(X, X_2) \to C_*(Y, Y_2) $. $f_\#$ commutes with the maps at the relative chain level $q_\#$ and $q'_\#$, that is $f_\# q_\# = q'_\# f_\#$ (this just follows by definition of $f_\#$). Since, the arrows commute at chain level, they certainly do at homology level.
$h_*$ is the excision map (an isomorphism). So, it commutes with $f_*$.
Lastly, you agreed in the comments $f_*$ commutes with the connecting homomorphisms for the LES of pairs $(X, A)$ and $(Y, B)$. In particular put $A = X_1 \cap X_2$ and $B = Y_1 \cap Y_2$ [Observe that $f(X_1 \cap X_2) \subset Y_1 \cap Y_2$]. So, $fd = d'f$.
So putting it all together, we get $f_*D = D'f_*$.