There is a way to do as you are attempting, however before getting into 
that have you looking into separating your processes.

  By your description, in pseudo code you are doing this procedure:

 

--[script.py

  01 - Import shaders

  02 - perform application

  03 - render

[bash-01]>./script.py

…Result: rendered images

 

By using the shipped in Render command you can find in your installation 
you already have granular control over your renders, so the procedure would 
be:

--[script.py

  01 - import shaders

  02 – perform application

  03 – save new version of scene

[bash-01]>./script.py

[bash-02]>./Render scene_version.mb

…Result: rendered images

 

  ////

  Same result but saves you a lot of code building if you do it like that 
and you have off the shelf distribution capabilities.  But if you still 
want to then each flag that the Render command uses is also accessible 
within python of course


http://download.autodesk.com/global/docs/maya2014/en_us/CommandsPython/render.html

  { If you use this one just batch and split your operations within your 
code and you have a batch renderer }


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