Reseated the cards at the back?
You could convert it to a 14 disks on single channel shelf rather than one split 7+7 by replacing the SCSI interface with the one that doesn't split the bus in half but that's not going to get past the problem of the shelf not responding.
Perhaps the RIS on the disks that you still see (internal) have been updated to know about the shelf and extra disks and it's that that the message refers to, adding an enclosure plus disks to a smart array controller makes it add knowlege of those extrernal disks to any other disks that are connected to it.
If you remove the extra controller and the enclosure does it still complain on boot?