As I'm sure you know, Unity 5.5 is using a new serialization version for GameObjects. This is causing .unity and .prefab files in BINARY mode to generate the appropriate error "These files require a newer version of Unity". However, when you set your project to TEXT mode (i.e. if you use GIT), no error is generated. And instead all the scene data is loaded with blank strings and names, with the GameObjects disabled.