Windows (Boot Camp) won't boot from HDD in optical drive bay I have a mid 2012 MacBook Pro, and I have done the standard mod of replacing the original HDD with a SSD and shifted the original HDD into the optical drive bay.

I then installed macOS onto the SSD and wiped the original HDD ready for Boot Camp. Now Boot Camp would not install to the HDD in the second bay, and the recommended steps from Apple was to disconnect the SSD temporarily, install Windows and then plug it back in. Worked like a charm.

Issue is not that I cannot boot into Windows. When I try to boot, I am greeted with a black screen and a blinking cursor, and that's it. Left it for a good 5 minutes and it didn't budge.

I am assuming it is because the boot loader on the primary SSD needs to have the information to boot into Windows, but since it had to be disconnected to install Windows on the second HDD this was obviously missed.

I have tried the common solution of booting into the Windows install usb, repair windows and running some boot.exe commands to try and repair but alas it does not fix the issue.

Any suggestions? Is it even possible to have macOS and Windows on two completely separate HDD/SSDs and still boot them in parallel?
You have not begun to given enough information to correctly diagnose your problem. This answer this therefore is based on many assumptions.

I know Windows 10 can be installed using the EFI boot method on the newer Mac computers. I do not know if this includes your model. Although, if your Mac does support booting Windows via EFI, then, I believe you should not of had any problems booting.

I have read from some Apple web sites where Windows can be installed on a second hard disk by temporally replacing the first disk with the second disk. If such instances, Apple referred to the computer as a Mac Pro. Your computer is a MacBook Pro. Mac Pro computers are designed to support a second internal HDD or SSD. Your computer probably was not. 

For the rest of this answer, I will assume you tried to install Windows to boot using the BIOS method. It would seem that if you are intent on keeping OS X and Windows on separate internal drives, then the answer would be to install Windows on the first drive and OS X on the second drive.

Another option, if the BIOS boot method is to be employed, would be to boot Windows from the first drive while keeping most of the Window on the second drive. To do this, you would have to create a small NTFS formatted "System Reserved" partition on the first drive. This partition can be as small as 100 MB, but 500 MB is the recommended size. This partition would also have to be marked as the active. This would also mean the first drive would be using a hybrid EFI/MBR partitioning scheme. The second drive would use the legacy MBR partition scheme. Once the "System Reserved" partition is in place on the first drive, you can simply boot the Windows installer from the USB flash drive and install Windows 10 to the second drive. The installer will automatically know which files need to be placed in the "System Reserved" partition. 

If you answer questions about setting up a "System Reserved" partition, let me know.