Hey sorry probably too late to help you, but I've just gone through this process for myself. I found that the better way to do this is to scan the the ROMS into Launchbox BEFORE you copy the CHD folders into the ROM directory. That avoids the duplicates in Launchbox and the games all still work fine if you copy the CHDs over after the import (because it's MAME that looks for the CHDs, not Launchbox).