Oh no!
That's
not what a 'sandbox' does -- it's not designed to 'only copy user data'. Quite the opposite -- it doesn't copy user data at all (you'd want to use "Backup - user files" for that).
A Sandbox creates
links to share the information specified by the script (either "user files and applications" or just "user files"). If that link replaces an existing folder, it doesn't explicitly 'remove' the files, but it does replace the folder with the link... it's basically overwriting an 'old' thing with a 'new' thing (of a different type -- the 'new' thing, with the same name, is the link that the Sandbox creates).
Fortunately, you didn't do an 'erase-then-copy' -- it's quite likely that the files are still on the drive. Data Rescue II -- from Prosoft Engineering -- should be able to recover them...
I hope that helps.