How can I install Windows on a second drive without disrupting Linux?

You can change EFI partition flags with a partitioning tool, but I wouldn’t treat that as the primary safeguard. Hiding the existing EFI partition can make Linux harder to boot temporarily and may not prevent every installer-related mistake. A full backup and disconnecting the Linux drive are safer than relying on partition flags alone.

If you leave both drives connected, carefully verify the target disk and partitions in the Windows installer. You can also arrange for Windows to use a separate EFI partition on its own drive, but the installer may still choose the existing one if it finds it. Temporarily unplugging the Linux drive is less convenient, but it’s the most reliable way to avoid modifying Linux’s boot files.

Installing Windows first isn’t strictly required. With UEFI systems, either operating system can be installed first, but Windows may add or change boot entries and sometimes place files in an existing EFI system partition. Make sure you have a backup and know how to boot the Linux drive directly from the firmware boot menu.

The safest approach is to temporarily disconnect the Linux drive, install Windows to the second drive, then reconnect Linux and select its drive as the default boot device in the firmware settings. After that, you can refresh GRUB so it detects Windows. This gives each operating system its own EFI partition and prevents the Windows installer from accidentally using Linux’s.