1 pointI think mdgarnett should do a Copy Media Set, with the destination Media Set a new one whose first Member is on the larger drive. Instructions for doing this are on pages 137-139 of the Retrospect Mac 14 User's Guide. Instructions for creating a new Media Set are on pages 87-90. Obviously mdgarnett will have to change the Destination Media Set in scripts that reference the one on the smaller drive.
1 pointFirst, this post by the very knowledgeable Lennart_T (formerly known as Lennart Thelander) says there is a 1TB limit on File Backup Sets. They do exist, but they are a pre-Retrospect-Windows-8 facility you should not use; you should be using Disk Backup Sets instead. Second, the "Scalable data protection" feature announcement for Retrospect Windows 12 says"Retrospect is now certified to back up 1 billion files per backup set, 100 TB of data per backup set, and 50 million files per device."