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Sure you can put a newer RAID controller in this system. It depends on a couple things though. Are you wanting to keep the data on the RAID array controller by the SRCS28X? If so that's a tough one. The SRCS28X uses the Intel* 80331 I/O Processor. Newer Intel* RAID controllers use LSI ROC controllers. This means that disk data is different and a newer controller wouldn't read the array configuration off the disks properly and let you just plug and go.
If you have a backup of your data, or can get one, and plan to start fresh and restore to a new controller, that's much easier.
I suggest a RAID controller that's compatible with the S5000VSA. You can find validated controllers on the S5000VSA the Tested hardware list.