So I was frustrated enough that I just downloaded the unreal engine source to figure out what was going on. Turns out the build tool looks for the registry “HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows Kits\Installed Roots” for KitsRoot10, which points to the 64bit version. However, as far as I know there’s no 64 bit include/source for Windows 10 SDK. So it’s looking in the 64 bit for includes/libs/sources instead of the x86 folder. I manually changed KitsRoot10 to point to the x86 folder (so Program Files to Program Files (x86)) and things seem to be going smoothly, though this might indirectly break other things. Hopefully this helps other people with this issue and maybe in the future the build tool will also check both the 64 bit registry and then the 32 bit registry.