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Windows has a lovely “feature” where it installs the bootloader on a secondary drive if there’s one connected. It doesn’t install it on drive 1 and drive 2, just drive 2. I always disconnect all secondary drives before installing windows for this very reason.
That said you can configure the windows bootloader to recognize your Linux (or grub) and just use that to manage booting two OSes and it’s less likely to not destroy things.
How can you do that?
Something along the lines of this
Supposedly easybcd supports efi now so you should be able to use that to do all the config.