Current Fedora 19 installation is on an Adaptec 29320 and I am trying to temporarily replace it with an Adaptec 29160. The functionality of the cards is very nearly the same except the replacement is U160. All the other drives, ID's and configurations remain the same. About half way through the boot process everything stops and I get dropped to a dracut prompt. It gives me the UUID's of two devices(disk partitions) it says it can't find. These are the partitions for swap and for the root file system. Using a different SCSI controller seems to create a different UUID that doesn't match what's in the initramfs. It appears that the dracut prompt is giving me the opportunity to create a new initramfs right on the spot that will allow the boot process to continue. But I would need to know what parameters/options etc to give it. I went back into my installation and regenerated the grub.cfg using the variable GRUB_DISABLE_LINUX_UUID=true. The new grub.cfg now has root=/dev/sdc2. But this only gets me a little further in the boot process.
A RAID controller cannot change the uuids of your partitions. It can, however, change the way in which RAID devices are constructed; that is, what they use as on-disk format, how disks are synced between each other, etc. Even controllers from the same brand are not at all guaranteed to use the same on-disk format.
If you're booting from the RAID, but then things fail after loading the kernel etc, then that would appear to mean that either the new RAID controller used a similar (but not identical) on-disk format, or (far less likely) that loading the driver and initializing the hardware changes the mode in which the controller works, causing it to look at the disks in a different way. Either way, you clearly cannot use the array created with one controller after switching controllers.
It you do want to do so, the only way is to put in the old controller, back up your data, swap controllers, reinstall, restore your data.