Hey there, Winterlord.
When you've installed Windows on your new SSD (which you want to permanently use as your OS drive), did you remember do disconnect all other drives during the installation process? If "no", then there might be some files written on one of your secondary drives and thus creating a conflict. Also in cases like this one, there's a chance that you might not be able to boot to Windows properly if you remove one of your secondary drives (which includes formatting as well).
If you've installed Windows on the SSD with the HDD connected to the motherboard during the installation process, then I'd recommend that you backup any important data which you might have on both drive, disconnect the HDD, make a fresh install of Windows on the SSD, connect the HDD and reformat it. After that go ahead and transfer back all the backed up data from that drive. This way you'd have a fresh installation of your OS with a fresh secondary storage drive and no leftover system files and partitions.
If you've installed Windows on the SSD with the HDD disconnected during the installation process - just backup all important data which you might have on the HDD and try to reformat it, then transfer back the data you need.
Note that if you are still unable to format the HDD, you might try to run a low level format (a.k.a. Write Zeros). This would erase everything on your drive and make your data irrecoverable (so as usual, don't forget to backup all of your important files before you try that). Basically most of the HDD diagnostics tools out there have that option. You could also do that via DISKPART. Here's how to do it:
1. Open CMD (Command Prompt) as administrator.
2. type in
diskpart and press "enter"
3. type in
list disk and press "enter", you'll see all the storage devices connected to your computer and you should be able to recognize the drive you wish to format, by its size.
4. type in
select disk X and press "enter", where X is the number of the drive you wish to format, so make sure that you've selected the correct one - e.g. if the drive you wish to format is disk 1, type in
select disk 1
5. type in
clean and press "enter", then wait for the process to finish.
After that your HDD should be initialized, partitioned and formatted as you see fit. Here's how to do that:
How to initialize or write a signature to a secondary hard drive or Solid State drive in Windows and
How to partition and format a WD drive on Windows and Mac OSX.
Hope that helps. Please let me know if you have any questions whatsoever and
backup your important data before you try anything.
Boogieman_WD