Your question intrigued me, as the fact that you say it is a hardware RAID should not affect the upgrade of Windows. As a hardware based RAID, the OS is only presented with the logical volume created by the RAID controller and everything behind that volume is abstracted from the OS. Windows should not know about, or even care about the Intel Rapid Storage RAID.
As I said, the problem piqued my curiosity and I did some Googling. The root of the problem may be the Intel Rapid Storage driver. The driver allows Windows to interact with the abstracted hardware. First thing to do is make sure you are running the latest version of the driver and related software. Upgrade to the latest version if you are not and try upgrading Windows again. Also make sure the BIOS for the motherboard is up to date. In addition to that, make sure any other firmware or BIOS for the Intel Rapid Storage is also up to date. It could be as simple as that, hopefully.
I do want to note that in my Googling, I found that some older Intel Rapid Storage controllers do not have drivers that are compatible with Windows 10. If this is the case with yours, uninstall the driver and related software. And try upgrading to Windows 10. For some people having this issue, this is a solution. Again, since the hardware is abstracted from Windows, you do not need the driver. You will not be able to interact with the RAID settings from within Windows, however you would still be able to to from the RAID controller's BIOS.