if you are booting off the silicon image controller, then anything you do to the intel controller is not going to affect the boot drive at all. you should be able to change the intel controller to raid, have the system start, and it should tell you it needs a driver for the new mode of the intel controller, from within the OS.
the only problem i see that could occur is if something important to the boot drive was lost when the intel controller was changed. maybe there was a bootmanager, or dual boot routine that resided on the intel controller at one time? something tying the boot drive to the data drive somehow, and it is not there when you change the mode on the intel controller.
check your boot order.... yes that is first to check. and make sure you are still set to boot from silicon image controller first in bios.
but beyond that you should be good to go, unless there is some anomaly like i described above.
Last edited by bdub
on Tue Feb 19, 2013 7:36 am, edited 1 time in total.
my main rig...
asrock 970 extreme3
AMD athlonII X3 440
zalman cpns5x performa hs/fan
crucial ballistix 2x4gb sport ddr3-1333
powercolor ax7750 1GBK3-H vga
antec neo he 650r
Samsung 840 EVo SSD 120 GB
toshiba 2TB HDD 64M cache sata3
seagate 1TB HDD 64M cache sata3
hitachi 2TB HDD 64M cache sata3
lg wh14ns40 bd burner
optiarc ad-7240s sata dvdrw (nec chipset)