Windows moved the bootloader to another drive
UPDATE I disconnected the second disk, restarted, and windows booted into repair mode instead of normally. I chose "startup repair" but it didn't work. It said windows couldn't repair automatically. The error detail shown was something like "NoOsLoader". I inserted the original Windows installation DVD and restarted the PC. In BIOS it said "press any key to boot from DVD", so I did that and booted from DVD. Selected timezone and keyboard, then chose "startup repair" again, and it fixed the missing bootloader without having to perform a full reinstall. Now windows restarted again and this time it could boot from C: normally. During all this time the secondary HDD was disconnected (both power and data cables) for just in case windows repair utility decided to mess with this disk instead. After repair was confirmed sucessfull, I connected again the other hdd and booted into linux. I inspected the D: partition and I found some files that were not there before and were created by windows recently:
/boot
bootmgr.exe
So that was definitely the cause of the problem. Windows HAD MOVED ITS OWN BOOTOADER TO A PARTITION OF HIS CHOICE.
I deleted those files as they were already reinstalled into C: where they belong.
Now to prevent this from happening again I have 2 choices:
- Never ever install "security" updates again, as they clearly mess with the bootloader.
- Disable the D: partition in windows.