Hi guys, need some serious help on this one.
I tried copying the unity project I have from one computer to another (via network, and also through a flash disk). Now weird thing is, after reimporting the project, some of my scenes are messed up: fog is off, shadow is disabled, some of the assets are placed randomly around the scene, etc.
Any ideas why this happened? BTW, we’re using a copy of Unity3D’s own asset bundling script.
Thanks! 
I guess it’s better to export your assets as package then open a blank new project to import the package. Still you need to do some resources linking such as tags may be missing.
I’ve encountered similar problems when moving projects from Windows to Mac.
Like Kenny pointed out, best bet is to package up and import. Or start a new project and then copy paste the assets folder and then build the scenes and reconnect dependencies yourself.