The selection set should be saved with the file so I don't know about that.

Assuming these are the final shaders, per face shader assignments are messy to manage and likely to create messy looking shading because the hard lines that will separate the shaders will often look rather odd. I do this only when projecting and laying out UVs, I have several solid color lamberts so I know what chunks of faces have been mapped. Otherwise the model will consist of separate parts that are grouped practically, then those groups will be under a parent node(like a curve), this enables easy selection, repositioning and shader assignments.