I disabled my LAN adapter for some reason a while back. When I re-enabled it my windows froze. I tried everything and finally removed the network driver from safe mode and reinstalled it again and it worked. I realized my secondary HDD was not detected anymore. The PCI simple communications driver was also missing and reinstalling the chipset driver did not solve this issue strangely. I have solved the PCI driver issue using third party software but the secondary HDD is still not detected. With the secondary HDD connected it takes a long time for windows to boot up.
I can access the both HDDs through Ubuntu booted from a usb stick and I have run extensive tests on it through UBCD(Ultimate Boot CD) and no error shows up.
TLDR; The HDD shows up in BIOS and on any other OSes but nowhere on Windows. Not on the device manager, disk management etc.
EDIT: I am using H170M-PLUS motherboard and my OS is Windows 7 Ultimate