Animation and FX pipeline for team project

We are trying to settle a flexible pipeline for our production.
Basically we have a Lib dir and a Scene dir. In the Lib dir we put the character setup and all our reusable animations.
In the Scene dir we group link all our chars’ setups and assign them the animations we want by making the setups “proxy”. Everything works fine, for compositing we simply link all objects from the animation scene so we can move characters individually among layers and start compositing. But for FX like smoke or dynamic paint we need to put modifiers on some meshes. As we have linked everything Blender will not allow us to do that.
We have tried to “Make duplicate real” on the meshes but as we have proxy armatures it makes weird things, some meshes loose their animation, it mixes up all the scene.
The other way to get over that problem would be to append parts of the setup and assign animation so we can use these as “clones” to put modifiers for instance. But it would be very tedious for large scenes with lot of characters.

here is a scheme of our pipeline to clarify what i just said :

thank you for your help