I was able to send this problem to a friend who figured it out. It is a simple fix with one input argument.
x = 1:10;
y = x.^2;
figure(1) % original y limits
plot(x,y)
[hplts,hax2] = addaxis(x,zeros(size(y)),'linewidth',1.5);
figure(2) % changing the y limits to [0 10]
plot(x,y)
[hplts,hax2] = addaxis(x,zeros(size(y)),[0,10],'linewidth',1.5);