rsync is used by to copy files remotely and locally

rsync -avzu /home/x /y

-u = do not overwrite a file at the destination, if it is modified

Source: http://superuser.com/questions/409980/sync-two-local-folders-in-bash

Or  you can use

cp -r -n /home/x /y

-n, –no-clobber
do not overwrite an  existing  file  (overrides  a  previous  -i
option)