Use the function 'open' to load the saved figure to a variable (a handle) and use yyaxis to add the secondary axis
figure;
axes;
x = linspace(-4*pi,4*pi,200);
plot(x,sin(x))
savefig(gcf,'newfigure.fig');
nf = open('newfigure.fig');
yyaxis(nf.CurrentAxes,'right');
plot(x,cos(x./3))
