$\def\pd{\partial}$ $\def\l{\left}\def\r{\right}$ $\def\mdot{{\dot{m}}}$ $\def\eps{\varepsilon}$ Consider a tube with longitudinal coordinate $x$ from $0$ to $l$ and varying cross-section $A(x)$. Derek S. Bale (a former student of Prof. Randall J. LeVeque) gives in his PhD (http://faculty.washington.edu/rjl/students/dbale/thesis.ps.gz) the Euler equations for density $\rho$, impulse density $(\rho u)$ and total energy density $e$ in such a tube in the form $$ \begin{array}{ccccl} \pd_t \rho &+& \frac1{A}\pd_x(A(\rho u)) &=& 0\\ \pd_t (\rho u) &+& \frac1{A}\pd_x\l(A\l(\frac{(\rho u)^2}\rho+p\r)\r) &=& \frac{A'}{A}p\\ \pd_t e &+& \frac1{A}\pd_x\l(A(e+p)\frac{(\rho u)}{\rho}\r)&=& 0 \end{array} $$ as an example for a spatially varying flux function.
Thereby, the pressure is determined by the gamma-law $p =(\gamma-1)\l(e-\frac12 \frac{(\rho u)^2}{\rho}\r)$. Note, that I have slightly reformulated the system such that beside the pressure $p$ only conserved quantities are used.
But, is it not better to change the conserved variables to the mass per length $m':=\rho A$, the mass flow $\mdot:=A\rho u$ and the energy per length $E':=Ae$?
As an intermediate variable one could introduce a pressure force $P:=A p=(\gamma-1)\l(E'-\frac12\frac{\mdot^2}{m'}\r)$.
Euler's equations reformulated with these new conserved quantities are: $$ \begin{array}{ccccl} \pd_t m' &+& \pd_x\mdot &=& 0\\ \pd_t \mdot &+& \pd_x\l(\frac{\mdot^2}{m'}+P\r) &=& \frac{A'}{A}P\\ \pd_t E' &+& \pd_x\l((E'+P)\frac{\mdot}{m'}\r)&=& 0 \end{array} $$ In this way one obtains a system with the structure of the original Euler equations (including a source term) where the flux function does not depend on the spatial variable. Therefore, the numerics should work fine. I could use Roe's method on this problem.
Do I miss here something?
EDIT:
Bale uses the first form to calculate supersonic waves through a tube with a narrowing halfway. The speed-up in the narrowing causes a supersonic wave and the corresponding shock wave.
The variation of $A(x)$ is smooth: $$ A(x) = \begin{cases} 1& \text{ for }x<1\\ 1+\frac\eps2\bigl(\cos(\pi(x-1))-1\bigr)&\text{for }1\leq x \leq 3\\ 1&\text{for }x>3 \end{cases} $$
I am aware of the fact that smooth transformations of the conserved quantities, such as $(m',\mdot,E')=(A\rho,A(\rho u),A e)$ have the potential to change the structure of discontinusous solutions.
But, is this really the case here?