If you would post your definition of R, that would help. Otherwise,
when I copy your expression for dRdtau_sq and try it, everything works
for me in the current master branch:
var('tau xth th')
f=Function('f')
g=Function('g')
y=D(g(tau), tau)**2 - D(f(tau), tau)**2 - D(th(tau,
xth),tau)**2*f(tau)**2
print y.subs((g(tau).diff(tau))**2-(f(tau).diff(tau))**2,1)
print y.subs((diff(g(tau),tau))**2-(diff(f(tau),tau))**2,1)
-> outputs
1 - D(th(tau, xth), tau)**2*f(tau)**2
1 - D(th(tau, xth), tau)**2*f(tau)**2
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