The following is best practices. Essentially, all you should really *need* to do is make sure that the unit ID is correct, and then physically replace the controller. It should take all its configuration information from the disks themselves.
But - to be safest, this is what we recommend:
Check the unit ID. On the rear panel of the controller is a pair of dip switches and tiny LEDs to let you know which is unit 1, and which is unit 2. All replacement units come default as unit 1. If you are replacing unit 2, check the dip switches on the unit 2 you're replacing, and make sure that you set them to match those on the replacement unit.
Power down (use the shutdown command) the defective controller you want to swap, then mark or note the cables positions and then uncable them (they need to be placed in the exact positions after controller replacement), unrack and remove it. Put the new controller in its place, re-attach all the cables. If the disks are spun up, you should be able to apply power and have it take its place in the system.
Note, if you're doing this online, make sure that the hosts are able to failover properly to the partner controller.
Check firmware and update if necessary. The S2A9900 controllers can run on different firmware, but should be brought up to the same firmware level as soon as possible.
The replacement controller may come up out of sync and thus be marked FAILED. No problem. Simply issue the command
from the partner controller or
from the failed controller. That will bring it back online.
Replacement of the controller is complete.