My old 360 died and I'm using its 20GB HDD for my new arcade 360. I just tried playing Ninja Gaiden Black but on the start up game menu it says "unable to load game settings. they will be rewritten. Press A to continue." If I press A will I lose all of my saves? I unlocked all of the costumes and really don't want to do it all over. If yes, is there a way to get around this?

No way to know if you dont try it. Making a backup of that save wouldn't be a bad idea. I wouldn't bother though.