I've checked on the Clonezilla site and there have been questions apparently but it doesn't seem enough people use IRST to come up with an answer.
I use Clonezilla (Linux live distro) to back up images of computers because the version of Ghost that we have does not support UEFI partitions.
If you back up a computer and try to restore it to a computer with a RAID 1 Intel Array, Clonezilla restores the image to 1 drive in the array and the array comes up with a missing drive that has to be rebuilt.
When using Ghost, I can load an image into an existing array, and it boots up clean with the array being stable.
When doing it with Clonezilla, it sees SDA and SDB drives rather than a single drive that would be the array.
I would assume there could be some Intel driver that is not loading, causing LInux to treat the drives as individuals, rather than an array, or maybe some kind of array device that Clonezilla is not aware of. (I.e. maybe it is only looking for SDA,SDB and not some other type of device node)
Since Clonezilla is a third party tool and we do not have any documentation regarding the possible results from using this tool, I would recommend cloning the partitions and then create the RAID from the Intel® RST software.