Just to chime in, I recently added a 48 to my "10 Gig" Mk.2a. The actual drive as shipped from Empeg was a 12.0GB Travelstar, and I added the 48GB Travelstar with no trouble.
The hardest part of the install was finding a 2mm jumper.

I disconnected the 12GB, connected the 48GB, ran the new builder, followed by the current beta developer build, and then added the slave jumper and reinstalled the 12GB.
No problems reported; all appears well, it seems to be booting from the 12GB, and as of now there's about 6GB of music on the second drive.
(Though, the drive= advanced search doesn't seem to work in emplode...)