Is there any issue with having windows on one drive and Linux on the other and toggling in the bios at boot? Do I introduce any problems by keeping my rarely used windows installation on a separate disk like this?
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I'm not sure, but clearly something happens on the background, as my Debian drive broke after I changed it back and forth for the Windows drive. Grub fell back to rescue mode. After following some instructions and trying to boot from grub command line, Debian wouldn't boot after it recognized the mouse. That's what I know. Even in different drives, something happens on the PC when you go back and forth with Windows and Linux.
I should have been more clear,
Assuming dev/sda is Linux and dev/sdb is Windows, I have grub on sda and Windows bootloader on sdb. I use a hotkey at boot to tell the bios which drive to boot from.
Theoretically windows thinks it's the only OS unless it's scoping out that second hard disk.