I've done this a bunch with IDE controllers, onboard and cards... If you're able to disable that onboard scsi card in BIOS, then the kernel should never detect it and then it will see the new scsi card the same as the old, probably /dev/sda1, sda2, then treat them as raid devices and detect them normally. It's no big deal really, watch dmesg scroll past on boot and see if it registers the new card with the right scsi ID, and if it doesn't, take note of where it is now, switch the drive back, boot, fix fstab and raidtab for where they will be, shutdown, switch, and you should be good to go.
Sometimes the kernel outguesses you. For instance I recently switched everything on my machine onto my ATA100 controller thinking that disabling the onboard IDEs in BIOS would keep the kernel from seeing them at all, it did anyway and I had to hack up my fstab as the boot drive went from /dev/hda to /dev/hde.
However, I've got a friends PPro with onboard SCSI, and I just disabled the SCSI from bios, put in a new card, switched the drives, and it kept its position as /dev/sda.
Alot of BIOS voodoo and luck is involved.
Cheers,
Finegan
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