I've got this scene with a few CoronaLayered materials set up like this:
[BASE MATERIAL] CoronaSurface1
[LAYER1 MATERIAL] CoronaSurface2
[LAYER1 OPACITY] File Texture
When I reopen the scene and hit render, it seems like the opacity map is being ignored and the CoronaLayered is only showing it's base material. When I reassign the CoronaLayered it works again as intended. Only noticed in Maya 2015, I will try to recreate the issue in Maya 2016 later today.