A late answer, but maybe this will help others. See my answer here on StackOverflow.com/Matlab. In this case you can substitute both variable at once via:
syms phi(t) Ja J0 x1 x2
J = J0-Ja*cos(2*phi);
dJ = diff(J,t)
dphi = diff(phi,t)
subs(dJ,{phi,dphi},{x1,x2})
You also don't need to define J as symbolic using syms since it gets allocated as such when you create the equation. I do usually like to make explicit the variable that I'm differentiating with respect to as well.
