i dont have a game the req 2 disks atm so i cant test , BUT .. when it gets to the point of asking , you should be able to just unmount the image , then mount the new , then hit ok in game. ....
well in theory ... this is still an alpha project.
in shenmue, the game saves, ask for next disc and continue
but if you want it saves, and before changinf, you can switch the dreamcast off and then swap disc, switch it on and then load it will continue with the right disc