A windows based raid setup

I'm assuming you're using 'motherboard' RAID, and you do not have an actual RAID hardware controller card.

If that's the case, reinstalling Windows, along with everything else, should not be a problem - the RAID simply displays a single drive (which is actually multiple hardware pieces of disk drives) to the computer (and thus, the OS). It's parameters are set at a 'lower level' than even the operating system.

What I AM confused about, as your problem isn't really clear, is whether you have a single drive (with the OS on it) or you have two separate drive systems, one with the OS and the other with data.

If you have 2 separate systems (I do this for example), then I'm actually unsure of the consequences - if you reinstall the OS drive, in principle I believe ( NOT NOT NOT sure) the RAID array should be recognized.

I know that with hardware RAID controllers, this is definitely the case, as they are coded in their own BIOS.

For software/motherboard RAID, I'm not sure.

whether the raid gets detected by windows setup program all depends on if windows has the drivers built in. If you didnt have to install them before then you wont have to now but if you needed them before you will definitely need them again.