Good point.
If you have set things up locally as per the video - then on your remote site you would need to delete :
components/com_fabrik/
administrator/components/com_fabrik/
media/com_fabrik/
and reupload the files to those folders from your local machine.
Alternatively there are online services such as deployhq (http://www.deployhq.com/) which sync github repositories to ftp locations
This deployhq thing actually looks really awesome. Now, would their system pull from your joomla 3 branch? Or would it still have to pull from my own fork?