Since the source for mfstools is not public, you'll have to guess based on reading its documentation.
My guess is, if you restore an old (original?) backup, you will lose everything that's happened since that backup was made (software updates, settings, recordings, etc.).
If you don't want to lose everything, you might look into backing up the 80GB drive and then restoring onto the 320 + 80 or just the 320 and put the 80 on the shelf.
The mfstools README doesn't seem to mention where swap goes on a dual drive system. Looking at the tpip-1.2 source, it looks like it'd be safe to tell it to write your swap headers on both drives (run it twice, once for each drive), and it should give you an error if either drive doesn't have a/the swap partition.