I have synced files around 1 Tb from one server to another and set up P4, but I have a different workspace in the new server so if i initiate a p4 sync in new server, Will it add only the difference or will it duplicate the files?(source remains the same)
Since you created a new workspace, and P4 doesn't know that you have the files already existing on your new environment, it will pull over all of those files.
If you kept the same workspace name, (by default) it would pull over only "new" files (because it thinks you already have the files you previously synced).