Sorry to bump this but I have a solution
first I'll explain my situation and little story
I have a custom rig I built with a MSI MOBO. I have a samsung 120gb SSD for the OS, and a few applications that i feel should go on the drive with the OS such as my AV, Malwarebytes, Firefox. I then have a WD Black 1TB as my main storage drive that all the other applications go on as well as videos, music, etc etc. I then point the shortcuts in the start menu such as music, videos , documents I point all of those to the main storage drive as I created folders in there to look like the ones in the C drive. For example, if you go into the main storage drive you will see My documents, program files (x86). Inside the documents folder is videos, music, etc. I point the shortcuts to those so when I click start and click on music, it will take me the music folder inside the storage drive, and not the OS (c: ) drive.
I then have a 2nd storage drive which is a HGST 500GB 2.5" that came from my PS4 as I upgraded the PS4 to a 1TB and didn't want the drive to go to waste. That folder has a downloads folder where all the firefox downloads go, as well as more videos, and stuff.
Anyway, after 10 years or a little more of owning WD drives, my first WD ever is failing. It has unreadable sectors and such so WD sent me a replacement drive. I don't have an external drive to back up to so I figured I would plug in as a 3rd storage drive, create a new volume, and make the drive latter J lets say. I would then drag, and drop the contents from the main storage drive ( d ) to ( j ). I would then shutdown, take out D, plug J up to D's spot, and then reboot, and then go in and change the drive letter from J, to D this way everything that is installed wouldn't point correctly, and it would be like I never swapped the drives. I would of course rather just clone it but because of the bad sectors I rather not do that.
Anyway, here's the part where everyone is having issues with which is similar to my issue. I plugged in the new hard drive, and the BIOS sees it but inside disk management it's not there. I then decide to shutdown, and unplug D, and E,( HGST ), just leaving J connected. I boot back in, and there it is. I create the volume as J, and I shut down, and plug it all back up thinking since now that windows sees it, everything will be seen.
I boot back up, and now I see my my C, and E, and J....no D.....the drive with everything I'm trying to swap over is not being seen. WTF????? I start getting a little annoyed. Now I have a nice empty drive but can't transfer anything to it because I can't access the old D drive. So, I decide to hotwire it in which means plug in the drive while the computer is on because sometimes that works as it has worked in the past for me. It pops up saying I need to format drive D to be able to use it???? WHAT!!!! I then click cancel but then disk management locks up and stops responding.....
I shut back down, and I unplug J, and I put everything back to the way it was before I even started but now windows is not seeing D at all. Now my main drive isn't showing........now I'm getting nervous because I'm not sure WTF is going on.
Long story short...^^^ lol.... turns out to be the SATA CABLES PEOPLE!!!!!! My MSI motherboard will only recognize WD drives using the two cables the MOBO came with, and not the other ones I bought to connect the other stuff. However, the other cables work fine with the HGST drive and my DVD burner. Just not the WD drives. Changing the ports don't do anything....it's the CABLES. I swapped my D drive back to one of the cable that came with the MOBO, and boom, it's all working again.
However, I'm not going to be able to have BOTH WD drives up and running at the same time to drag and drop until i go pick up some new cables to see if I can't get them both showing. For my case it's definitely the cables I'm using.
So, if you're having an issue with the BIOS is seeing the drives but windows is not.....try different cables......it's the cables.