I unplug physicals disks when installing windows. Learned the hard way when windows placed the boot partition on a device it could not detect the filsystem of. It destroyed my RAID disks (a little but my fault, because I messed up the recovery).

This is what Windows installer saw (going by memory, this was 8 years ago)

• SSD 500 GB (either it recognised ext4 file system, or this one was unknown)
• SSD 500 GB (Where I specified to install windows)
• 4 x HDD 8TB (unknown disks, unknown file system, Windows unaware that this was a RAID-5 software dm-raid)

What did it to? It created a new partition table and wrote data to a new boot partition it made on one of the 8TB disks, no questions asked.

So, to the people who answered you that windows installer cannot do this. Maybe they fixed it. But it certainly could, and it cetianly did. I remember very carefully going through the installer because I was concerned about this happening. I thought about unplugging them, but was lazy. Because "it would be insane for windows to write on a disk it cannot identify the file system of".

Lessons learned:

• If you plan to install windows on a disk along side Linux, install windows first, if you can. Safest bet is still to:
• If you cannot, unplug all other disks other than the one windows is intended to be on.

Edit: I found post on this way back when, but leaving what I wrote as is.

https://superuser.com/questions/758854/mdadm-win7-install-created-a-boot-partition-on-one-of-my-raid6-drives-how-to-r#1243636

I had remembered some details wrong. I had unplugged the Linux SSD, and it wad raid 6 not 5, and it was 2TB disks.