Replacing a drive is easy: add the new drive to the storage pool, then remove the old drive from the pool. Finally, remove the old drive physically. If you don't have room in your case, you can use a USB bridge device to connect the bare drive temporarily.
Add it, remove the old drive, and install the new drive inside the case.
If you have plenty of free space, you can remove the old drive first, then add the new drive afterward.
Cloning drives is unsupported and likely to cause problems, as Windows Home Server uses identifiers which don't usually get copied for it's storage pool drives.
I'm not on the WHS team, I just post a lot. :)