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My linux is Mint, but I think the issue is the same. I have this old AMD PC Gamer with Linux and Windows and traditional bios booting.

I had Linux 20 in a SSD in a SATA II port and Windows 10 in another SSD using PCI-e to SATA III adaptor (to get more speed). When I tried to update Mint 20 to 21, it got stuck in the middle. After a while, I decided to install Mint 21 fresh from a usb stick... bad choice! Windows won't boot anymore.

Problem is, the Linux SSD had the Windows boot partition, the other SSD have the Windows itself only, a NTFS partition only. I wish to add it to grub boot menu but os-prober won't find Windows, witch make sense with my low knowledge. However, I think if I use a Windows tool to rebuild a boot partition, it will mess with my grub and I will miss the Linux boot.

What should I do?

Gustavo
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Yes, Windows will takeover boot from grub if you try to let it repair on the disk that contains Linux.

I'd recommend to backup anything you need from the Windows disk (hopefully it's not bitlocker'd) to the Linux disk then remove the Linux disk while doing Windows repair. When that's complete you can use the solution linked below to update grub and see both again as boot options.

GRUB does not detect Windows