"they said its not possible to boot the new harddisk as the raid controller can`t detect" If the controller doesn't detect the disk, then it is not possible to boot to it, but obviously it is detecting it if you were able to configure a single-disk RAID 0 with it. In CTRL-R, the option to change the boot VD is on the CTRL MGMT screen. In order to boot to the cloned disk, however, you may need to repair your OS boot files (if your cloning utility isn't capable of preserving that info ... the fact that you cloned a larger "disk" to a smaller "disk" indicates you may have copied only the partition, in which case, the boot files would not have been cloned ... but that may depend on your cloning software).
 My Server Power Edge 1950 running server 2008 32Bit, using 3 Physical SAS HDD as a Virtual 2 Disk configured for RAID5, with partition of C drive as OS and D drive as Data. Planning to format and install Server 2008 R2 64Bit so i insert a New Physical disk and configured as RAID5 and clone the C drive and D drive to the new hard disk. now i need to test the New hard disk is it able to boot the windows and work as expected. How do i test, i am not able to boot the windows by choosing the new harddisk, the bios show only the existing HDD. not the new one. and also if i remove the old three hard disk, and leave the new harddisk and then am i able to boot the device, if i do this does my existing RAID5 configure and data in hard disk still remains.
Raid Secondary HDD Bootup