Shell Script Synchronise Folder with External HDD
This is easy to accomplish using rsync. 
The easiest route is to open terminal and type rsync -r and that drag the source folder to the window, followed by the destination folder. -r stands for recursive, so it will look inside the folder and its subfolders. I just synced a folder on my desktop and a mounted USB drive with this command: 

rsync -r /Users/My-User/Desktop/Test_folder /Volumes/My-USB-Drive/Test_on_USB


It actually creates the Test_folder inside the Test_on_USB folder. 
I'm not an expert on all the options, but you can find them here: http://everythinglinux.org/rsync/ 

Let me know if that accomplishes what you're after.