Would it work if, instead of copying in the exporer, i imported the same NGUI package in both projects, then exported? Does package itself contain metadata?
BTW, i got a script that restores missing scripts based on their serialized members and it works very well with everything except for most NGUI stuff. Is that because of you serialize things using some custom inspectors? Perhaps... Some script that would serialize prafabs into some JSON, based on script and asset names instead would be very handy