What version did you use for testing? I am on 5.4b13 (and I won't go back to 5.3.x). It propably got lost in my last posting, but the docs for 5.4 don't know of this ReflectionProbeUsage attribute, only the 5.3 docs do. Is this a 5.3 vs 5.4 thing?
EDIT:
I tested your code snippet. Now the error message is gone, but the children of the GameObject are still skipped. Does DataNode not serialize children automatically? I would have expected so?
Also the error still remains when I import a text-based node (instead of binary) and the GameObject is not recreated at all.
EDIT2:
I did some more testing and had some interesting results. Instead of using my own assets I simply exported a default particle system. When I load the DataNode back I got
this bug, where the loaded particle system is there, but the material is lost so everything is pink. In that link, read my oh-so-delightful exchange with Unity support on this.
Here I described my workaround.
Workaround 1: To export from OpenGL Core -> OpenGL Core on Mac, force-include the built-in shaders in the Graphics settings. This was for asset bundles workflows on Mac OS X with Unity 5.3.x. Now the thing seems back with DataNodes on 5.4b? Including shaders in the Graphics settings does not help. Workaround 2: Force OpenGL 2. These workarounds do not improve things with Unity 5.4 and DataNodes.
When I export the particle system as text the material related lines say:
sharedMaterial = "asset|Material|unity_builtin_extra"
sharedMaterials = string[]
asset|Material|unity_builtin_extra
As a next step, I will test asset bundle import/exports. Would be too funny if they not only did not fix stuff in 5.4, but even killed the workaround.