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i use a different drive for my windows installation because that happened to often,
and i swear it once managed to wipe the bootloader on the linux drive.i have no idea how it did that,
but i avoided starting windows using the grub entry since then.Having two drives is sometimes not enough, either. I have no idea why, but anytime Windows installs for the first time or goes through a major update (not the small security patches, but the periodic feature releases) there's a random D20 dice throw to determine if it will randomly decide to create the bootloader and recovery partitions in another drive, even though your main installation isn't there.
I kid you not, Windows 10 once decided that my external SSD enclosure was the best place to put the bootloader.
This happened to me! Did an update, unplugged my eSATA and BAM! Can't find bootloader. I literally, physically facepalmed when I realized what happened. At least the old one still worked from the primary.
I've done a ton of Linux updates and this has never happened to me once (yet).
