So right now I am working on a project with two 2tb hard drives. One is almost dead so I needed to buy new drives. I decided to get one 6tb hard drive. I got this: Western Digital 6TB My Book Studio Edition II HDD WDH2Q60000N0 (http://www.adorama.com/WDH2Q60000N.html?utm_source=RSYS&utm_medium=TransactionalEmail&utm_campaign=1point0product)

I need to transfer the data but do so in a way that I do not remove all the links between the data and where it is located. Any advice on how to do this?

I would copy the whole folder structures to the new drive. You then have a choice:
1) Unmount the old drives and launch the project. FCP will say there's stuff missing and give you the chance to re-attach it all. There's a checkbox that lets you automatically reattach everything in the folder so doing the first, you get a whole folder's worth. It works. I've done it.
2) Unmount the old drives and rename the new drive to the same name as one of the two old ones. When you launch the project, you only have to do 1) for the files that were on the one drive

Hope that makes sense. There are the occasional problem files.