I just replaced my motherboard, and now my Windows hard drive (secondary) seems not to be detected. I'm running Ubuntu 16.04 on my main hard drive and Windows 10 on my 2nd.
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sudo update-grub
. That may bring the Windows bootloader entry back but it is unlikely to work. As commented before Windows needs reinstalling (or recovered) whenever the base hardware is changed and then re-activated. – Sep 10 '17 at 17:14