I've been having an issue where every time I install a Linux distro on my NVMe drive, it somehow ends up deleting the Windows bootloader that's installed on a completely separate drive, which is my SSD. The weird part is that the installation process doesn't seem to touch the SSD at all. For example, I can still access the small partitions on that drive, like the Recovery and System Volume Information folders. However, after installing Linux, I can no longer boot into Windows because the bootloader is completely gone, even from UEFI. Is there some kind of conflict between Windows and Linux that causes this, or is Windows just messing things up behind the scenes? Also, I found out that Windows was saving its EFI partition to the NVMe drive instead of the SSD, which is why it got deleted when I wiped the NVMe. I'd really like to know how to avoid this problem in the future without having to reinstall Windows every time I try a new distro.
5 Answers
I had a similar issue when installing Fedora 42. For me, it was all about the installation method. I ended up having to reinstall Windows after messing up the bootloader. If you're not careful, it can overwrite existing boot options on other drives.
It sounds like your Linux distro is using the existing EFI partition from your NVMe drive instead of creating its own. When you install Linux, try creating a separate FAT32 EFI partition on the Linux drive and make sure it has the right flags before installation. That might help prevent it from touching the Windows bootloader on the SSD. Also, consider changing the flags on the Windows EFI to msftdata when installing Linux, just to be safe.
I don't think that's the issue here. When I installed my setup, Linux didn't modify the SSD at all. It was Windows that placed its EFI on the NVMe drive instead of using its own. It ended up deleting the Windows EFI because Linux wiped it out during the install.
Always check where GRUB is being installed during Linux installation. Many distros will default to the active EFI partition on the first drive they detect, which could create issues if you have multiple OSes. If you want a foolproof setup, disconnect the SSD while installing Linux, that way it'll only see the NVMe drive.
That’s a hassle, though. I’d prefer to find a way that doesn’t involve unplugging my drives every time.
If the Windows disk wasn't disconnected during the install, it’s likely that the installer wrote GRUB files to the Windows EFI partition regardless of your selection. If you want to dual-boot, definitely read up on how to do it correctly on multiple drives to avoid this mess next time.
In my case, unplugging the Windows SSD wouldn’t have helped since it installed the EFI on the NVMe without me knowing. Windows just decided to ignore my input.
I've noticed that pulling all but the target drive when installing an OS avoids a ton of problems. But if you're not comfortable with that, just pay attention during the installation process and choose the correct partitions.
True, but that shouldn't be necessary. It's more about how the installers are set up to handle multiple EFI partitions, which can lead to these kinds of headaches.
Yeah, I used a USB to boot the Windows installer. It can be tricky if you don’t know how to set it up correctly.