Prefab Materials and Meshes being deleted, How can I stop this

In the editor I have created prefabs (A) in a resource directory, in code I am loading them, then instantiating a copy of it(A’), and creating(instantiating) a pool (array) of gameObjects (B), finally I am setting the pool items’ (B) material and mesh to that of A’.

This all works great the first time I run, but as soon as I stop, it appears that the clean up deletes (A)'s material and mesh.
Why and how can I prevent this from happening to a prefab in the project?

Again Project has prefab A, I load A and instance it to A’ then create B’s and assign B’s material/mesh to A’

such a useless system, it’s been 9 years and this person doesn’t get ANY freaking help.