If I understood correctly, the geometry does not change and only the pde coefficients change. If this is the case, I would recommend a one-time exporting of the mesh and the BCs from pdetool and saving it to disk. Then, rather than go through pdetool for defining coefficients, using the command-line function: assempde/parabolic/hyperolic, programmatically enter coefficients and solve. Of course you will also need to load the mesh and BCs from the matfile that you've saved to prior. This way you need to use pdetool exactly once.
HTH
Deepak
