I failed to mention that I have replaced certain portions of the meshed grids with NaN's themselves, so I don't neccessarily end up with a rectangular grid for the subset or the main set. This seemed to work, though:
Coord_A = G_A(:,1:2);
Coord_B = G_B(:,1:2);
for i = 1:1:length(X_A)
[id(i),locb(i)] = ismember(Coord_B(i,:),Coord_A,'rows');
end
Rbig = nan(size(G_A));
Rbig(:,1:2) = G_A(:,1:2);
Rbig(locb,3) = Z_B;
This seemed to do the trick.