Copying large amounts of files usually works fine with the 'cp' command but if there are any symbolic links in the files being copied you will copy the files being linked to instead of the links themselves. To solve this one can use the tar command like this...
tar cvf - * | (cd /destination ; tar -xvf - )
This will tar up all files/dirs in the current directory, pipe it to the commands to change directories to where you want the data to go, then untar the files in their new location.