Few days ago I decided I wanted to re-install Windows. There was nothing particularly wrong with my system, just that I prefer a squeaky clean machine (thanks to my OCD) and also I couldn't get Xilinx to run correctly, so I figured doing a fresh install might help.
The point being, anyone who's installed Windows on a machine that already has Ubuntu, would know that it erases the Master Boot Record (MBR). In other words, you won't be presented with the GRUB menu, so you won't be able to boot into Ubuntu again. This is a very well documented issue, and the simple workaround is to pop in a Live CD and reinstall GRUB. You can find out more about that here or here.
But turns out the guys at Microsoft have worse things in store.