The Dock aliases are just pointers to the open the original so you don't have to dig around in the folders to find it and launch it.
Once your done changing the original, drag the "?" off the Dock, then drag the original to the Dock (file, program or folder) and it will create a new "alias" in the Dock pointing to the new locaiton of the file. (original returns to it's original location)
Sometimes you have to move it around to find it's right spot, like the Downloads folder only goes near the Trash for some reason.
You move the original then of course you have to delete the alias and create another one.
https://discussions.apple.com/community/notebooks/macbook_pro?view=documents