You should have no issues. The RAID data is written to both the BIOS and the drives themselves. When you're done in AHCI land, go to the BIOS and set the system to RAID, then shutdown and plug in the drives. Boot back up and the system will now scan the drives and find your RAID configuration. This happens in just seconds. The BIOS will reload the RAID information back into the BIOS for safe keeping (and faster boots) and you'll be on your way. You may have to reboot after the RAID is found and go back into the BIOS to set the boot order of your RAID array so that you don't wait for card readers and USB drives to boot first

. Make sure you reinstall the drives in the right order, most RAID chipsets (even motherboard raid) can deal with the out of sequence drives and rebuild properly, but that's not always the case, best to be safe and plug them in the same order.
This is something very common. If you ever flash your motherboard's BIOS, you'll see everything goes to defaults. But when you turn RAID back on in the BIOS and boot as normal, your RAID will be there and perfectly fine.
As for experience on this: 3 MSI 890GX-G60 mainboards with RAID 0 arrays getting flashed from 1.2 to 1.4 then 1.6 BIOS's. Also ASUS M4AVT onboard RAID 1 arrays. Dell Perc 5 SCSI arrays, HP SmartArray SCSI setups, and LSI MegaRAID setups. Lots of RAID experience

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