Secondary Internal HDD Vanishes/Reappears Randomly In Windows 8.1

To clarify, I'm referring to entire disks disappearing, not just partitions. The PC in question is an HP Pavilion 2325DX. Both drives are variants of HGST. One is in the primary slot, the other is in an optical caddy. Partition style is GPT/UEFI. Each disk has 1 EFI partition (per disk). In Windows, the drive will be there sometimes, but sometimes gone after reboot. It only happens on the secondary drive, not the one Windows is installed on. It also seems to make no difference which slot each drive is in. My Linux install sees both drives perfectly all the time. It seems to be completely random. It doesn't happen often, just enough to annoy, and is hard to get it back again. This has perplexed me for over 2 months.

What I've tried:
1. Called HP, won't help unless I pay a hefty fee and won't give any info, PC is a gift and no longer warrantied.
2. Called HGST, they say they've never heard of such an issue, no firmware updates available, rep never called me back.
3. Swapped the drives into the other slot, issue went away for awhile then returned.
4. Installed all Windows Updates and latest drivers.
5. Tried Win 7/10, same issue.
6. Ran SMART/diagnostics tests, drives are relatively new and came up clean.
7. Put both disks into an external caddy, they read fine from Windows/Linux, and from friends' PCs.
8. Tryed varying partitions sizes of less than/more than 1TB, seems to have no effect.
9. Downgrading/Updating BIOS, no effect

I'm thoroughly confused in regards to what could be causing the issue and don't know where to start looking, new optical caddy is cheapest option but not guaranteed to work. PC is otherwise satisfactory in all other respects.

Thanks in advance!

Solution 1:

Another idea : Sometimes the problem is with the power supply. There are two cases :

1. The secondary hard disk is connected to a power cable which is shared with another device.
   If the other device draws a varying amount of current, it might not let the disk start up fast enough to be counted as up and running by Windows. The allowed startup times vary between different operating systems.

2. The Power Supply itself is barely enough for the computer and is sometimes not enough.
   Especially if some device sometimes draws more power than it is supposed to.

The first case can be verified by giving the secondary hard disk its own unshared power cable. The second case needs careful calculation of the power needs, remembering that the Power Supply might not be capable of really delivering every last Watt in its specification.

Solution 2:

1. Insufficient power on startup. Possible as ODD usually requires more power to work, but less or same while spinning up as HDD. But make sure - what is the nominal power consumption for the hdd in the caddy? Usual are 0.5 A/1.0 peak for hdd. Try disabling all devices - wifi for example. LAN, especially if configured wit network boot (PXE).. I would rule this out, though - you say it's always secondary drive that's missing then it's definitely software problem. And yes, that would include UEFI.

2. No matter which slot, windows missing secondary one. I'm not sure on Win8.1, but is there a way to designate drive as "permanent", as opposed to "removable"? It would normally have no issue on reboot (just on wake), but this is UEFI...

3. Power options in Windows may have something to do in connection to "removable media". Again: no issue on boot/reboot, just on wake.

4. SATA is designed as hot-plug compatible. You can disconnect and reconnect drives while system is powered up. Will Windows recognize it after that?

5. Windows 8 likes UEFI very much and when those two get together, they like very much to be ran in "Secure Mode". In my Dell days this option was responsible for lots of issues on it's own. Disable/Enable does the trick?

6. UEFI has it's own quirks. Sometimes going from UEFI to Legacy mode, reboot, switching back to UEFI and rebooting again clears a lot of issues with HDD recognition on start-up...