Dual Drive / Dual Boot Workstation - How to safely reinstall Windows without removing the drive and messing up my Linux installation?

Hello everyone,

I currently am dual booting Fedora 43 and Windows 10, with each system installed on its own separate NVME drive. I’ve enrolled my Windows installation for extended security support, but it ends next year - I’ll have to upgrade to Windows 11. I would like to reinstall Windows alltogether, and maybe even use an LTSC branch foir longer support.

I’ve read plenty of articles/tutorials on dual booting and all of them state that you should always install Windows first, which is exactly what I did. I installed Fedora afterwards, and have been dualbooting since - I even reinstalled Fedora, which didn’t affed my Windows installation.

Here’s my question: is it possible to reinstall Windows onto its own separate drive without it affecting my Linux installation? Most tutorials state that users should physically remove their Linux drive before installing Windows, and only add them later after installation is complete, because it messes up GRUB bootloader. Since both my systems are on separate drives, is it possible for the Windows installation to affect the boot partition on the other drive? Or can I safely reinstall Windows onto my Windows drive, and my separate Fedora drive will not be affected?

I will be very grateful for any help and input, especially from those who have successfully reinstalled Windows on dual boot systems. Thank you!

yes
no
maybe?

If you have the systems fully on separate drives, each with their own independent efi partitions, then it should be quite possible to reinstall windows and not affect the fedora OS.

To ensure the fedora OS is not affected it would generally be wise to disconnect the fedora drive before reinstalling windows. After reinstalling windows you would then have to use bios to boot fedora and repair the boot order.

If instead you have a shared efi partition that boots both OSes the process would be quite different.

Thank you for answering, Jeff!

I do have both systems on their separate NVME drives, each with their own EFI partition - to disconnect the Fedora drive I’d have to physically remove it from the motherboard, which is something I’d like to avoid - I’d have to physically remove the GPU as well to be able to access the slot.

I read plenty of horrible stories about GRUB getting wiped out from Fedora installation, but these mostly came from people dualbooting on a single drive. I wasn’t able to find much information about dualbooting on two separate drives, hence my question here.

It is pretty much a given that (re)installing windows will affect the bios config and mess with linux booting.

There are ways to recover, but you would be advised to search here for others that have already gone through what you are proposing and see what actions needed to be done for recovery before you begin.

This is just one of many on the topic

When I first started with Linux I thought since I was using separate drives I could install Windows after Linux, but I was wrong. I don’t remember what happened, but it was messed up. So I very much second the suggestion to physically remove your Linux drive when you install Windows.

Another option you could investigate is if you can disable your Linux drive in your system UEFI BIOS. I haven’t done this so you’d need to look into it, but it might be worth considering if you don’t want to open up your laptop.

Thank you very much for your help and the link - it seems that no matter what you do, Windows will find a way to mess up dual booting (in the link you provided the user disconnected his drive, and Windows still managed to mess up the boot partition). It’s very discouraging, since I need Windows to be able to run games with anti-cheat. :frowning:

Thank you for the suggestion! Sadly, I can’t disable my NVME drive in BIOS, but as per case in the link provided by Jeff it doesn’t seem it would do much good - even physically disconnecting the drive and reconnecting it can still result in issues. Sigh. :frowning:

Not true as long as windows is installed first in the system.
I have used windows and fedora dual boot on several different laptops and desktop systems for many years. Install windows first then fedora plays nicely with windows. Install fedora first and windows second → nightmares occur.

Oh, I realize that - that’s how I set up my current dual-boot workstation. Sadly, Win 10 will stop being supported in October this year, so I have to do it again…and it looks like there’s no easy way to avoid trouble :frowning:

On my windows 10 laptop it seems MS tries to force an upgrade to windows 11 and a reinstall is not required. I do not wish to upgrade so even though win10 support ended some 3 months back I am still on win10.

That is true - as you might recall from another topic I opened I had to disable TPM to avoid issues with shutting down/rebooting my computer while using Fedora, and TPM is sadly a requirement to use Windows 11.

I do not particularly wish to upgrade either, hence why I thought of switching to a LTSC version which manages to avoid plenty of regular MS bloat and offers longer support - however that requires a reinstall. :frowning: