Thinking more about this, the common thread seems to be that meshes/lights in the stack of prefabs and collections don’t show up properly until they have been adjusted or placed in the scene.
I’ve also tried a few different sequences of actions:
Duplicate top prefab >
nothing shows up on top prefab (no lights, no meshes)
Duplicate top prefab >
nothing shows up on top prefab (no lights, no meshes) >
save, close, reopen >
no change
Duplicate top prefab >
nothing shows up on top prefab (no lights, no meshes) >
place all the lowest prefabs (only meshes and particles) in the scene >
nothing shows up on top prefab (no lights, no meshes)
Duplicate top prefab >
nothing shows up on top prefab(no lights, no meshes) >
place all the lowest prefabs (only meshes and particles) in the scene >
nothing shows up on top prefab (no lights, no meshes) >
randomize the duplicated prefab >
meshes appear - lights don’t work
Duplicate top prefab >
nothing shows up on top mesh (no lights, no meshes) >
place all the lowest prefabs (only meshes and particles) in the scene >
nothing shows up on top mesh (no lights, no meshes) >
save game >
meshes appear on the duplicated prefab - lights still not working
Duplicate top prefab >
nothing shows up on top prefab (no lights, no meshes) >
place all the lowest prefabs (only meshes and particles) in the scene >
nothing shows up on top prefab (no lights, no meshes) >
save game >
meshes appear on the duplicated prefab - lights still not working >
go in to every light and adjust it (move then Ctrl+z undo is enough!) >
now both the meshes and lights are working!
Duplicate top prefab >
nothing shows upon top prefab (no lights, no meshes) >
place all the lowest prefabs (only meshes and particles) in the scene >
nothing shows up on top prefab (no lights, no meshes) >
save game >
meshes appear on the duplicated prefab - lights still not working >
go in to every light and adjust it (move then Ctrl+z undo is enough!) >
now both the meshes and lights are working! >
duplicate the duplicated top prefab >
meshes work, lights don’t >
save, close, reopen >
duplicate the duplicated top prefab >
nothing shows up on top prefab (no lights, no meshes)
So… That’s a few versions!