Its a good question that I've tried a work around for.
After you've copied all your samples over to your new hard drive do the usual process of running the
Scan setup process. From here where you would usually add a scan set just do a Edit scan set instead. From here just add your new destination disc to your original - just find the duplicate folder and add it to your existing scan set. Then scan both destinations again. You may get some doubling up of samples but at least its looked in both places. So you'll always see at least one destination from your database search.
Obviously a better solution would be to add a second Library destination to add to the database in Preferences to save a whole lot of re-scanning...