lost object in hierarchy! connections broken to objects?

Hey hey,

I have a scene in my game with quite a few objects and after an object wasnt updating from maya i clicked the "apply" button on the unity object, after that the ONLY object i see within that scene and the hierarchy is the object i clicked apply on.

then with other scenes using the same assets, some objects in the hierarchy are blue, showing an update connection, where some are white showing no connection.... NO IDEA WHAT IS HAPPENING!!!?!?!?!??!?!?!?!?!?

corrupted file??

PPPPPPPPPPPPPPPPPPLEASE HELP!!!!!!!!!!!!!!!!!!!!!!!!!!!!