Use the two handles replied by plotyy:
t = linspace(0, 2*pi, 200);
hAx = plotyy(t, sin(t), t, cos(4*t));
pause(1)
set(hAx(1), 'XDir', 'reverse')
pause(1);
set(hAx(2), 'XDir', 'reverse')
gca is the current axes object only, while the 2 axes handles replied by plotyy let you access both.
By the way, plotyy is outdated. Use the modern yyaxis instead.
