A Linux and Windows 8 user has reported on Reddit that one of the updates performed by Microsoft’s OS Windows 8 deleted the GRUB boot loader and set UEFI to secure boot. It was not Windows 8 to Windows 8.1 upgrade, but regular Windows 8 system update.
He claims that after the Windows System Update GRUB 2 was removed, and UEFI booting was set to “secure boot” which it wasn’t prior to the update. During the update, Windows 8 mentioned “there is a security problem with your computer” that needed to be “fixed”.
When user contacted the Microsoft support he did not get satisfactory reply. He also said that the Microsoft support representative also made the following statement: “MS updates makes sure W8 functions fine, it does not look at other OS’s integrity.”
After user restored GRUB2 he said that “now there are three different windows boot loaders besides the Linux entry, each on a different partition that wasn’t there before. Apparently, they have found a new way to fragment your disks entries besides the Linux”.
According to him, this happened on a Lenovo Ideapad Flex while dual-booting Windows 8 and Xubuntu 13.10. Unfortunately, he wasn’t able to pinpoint which update was to blame. Also, another user in the same thread said that he faced a similar problem when dual-booting Windows 8.1 with Fedora 20 and Ubuntu 13.10.It’s difficult to ascertain the veracity of these claims, but it wouldn’t be that far-fetched for an update to actually do all those things.
At the end he mentions,” Hopefully, this post will save other people from running into the same stuff. If you run a dual boot machine, turn off W8 automatic updates so you can at least try to vet them before they run.”
Windows is known for not detecting other OSes on the system and deletes the boot loader, but we have not seen any Windows update doing so. It could be a bug or a deliberate attempt by Microsoft to break dual booting Linux systems.