In my case, the 500gb drive is purely a data disc, with the OS living on one of the 1tb drives. Does that change anything? I don't plan to ever pull/replace the 1tb drive that the OS lives on, except if the HDD starts going bad and I have to replace it.
Your job should be easy. Add the new data disk to WHS. Then "remove" the old data disk from WHS (using the WHS Mangement Console). After WHS reports it's safe, you can physically remove the old 500 GB disk.
Whoops. I see you mentioned, "all four bays full". That does complicate it a bit more. You should be able to temporarily add the new disk via a USB or eSATA connection, and then move it to a SATA bay on the server. I haven't tested this one. I certainly wouldn't expect an eSATA connection change to result in a new Disk ID. I doubt that moving it from USB to a direct SATA connection would change the Disk ID, either. But I can't 100% guarantee this.
You could also temporarily add one or more other USB or eSATA disks to the server, "remove" the old 500 GB disk, "add" the new large disk, and then "remove" the temporay disk(s).
Or temporarily copy off across the network enough data so that you can "remove" the 500 GB disk. "Add" the new large disk and then copy the data back to your server across the network.
If you plan ahead while you still have 500 GB of free space on your other installed disks, you can "remove" the 500 GB disk first and then "add" the new large disk. If you have Folder Duplication enabled, you can also temporarily disable it to give you space for "removing" the 500 GB disk. After everything's migrated, you can re-enable Folder Duplicaiton.
All of these steps will take a while to finish, but they are automated, so you don't have to nurse them.