It won't affect linux itself, you can restore the bootloader and get into linux when windows does that, it's just that it's a pain in the arse to restore. But yes, it has happened not too long ago that windows overwrote the linux bootloader. Microsoft obviously claimed it was an accident, but they obviously don't care.
And no, on a separate drive windows won't touch it at all.
EDIT: Maybe it's not so hard to restore grub loader as I thought, could be as simple as these steps.