Newer HDDs won't mount after restart in Mac Pro 4,1 and 5,1....

Thanks @kahjot - I actually really liked the performance of the new WD 4TB drives, so that's why I've not returned them. I rarelly restart my machine and when I do I can discipline my self to turn it off and back on again until this get's solved.

After doing some more research and not restricting myself to just MAC I found that this also happens on Windows (and hence non apple HW). There have been several cases reported and the solutions that most often work are to enable hot-swap in the BIOS or to update the SATA controller's driver (usually intel) - both of which we can't really do in a MAC PRO running macOS X.

I've also seen that people running older versions of the Mac OS X also don't experience this issue... This leads me to believe that it may indeed be a driver issue then, that was updated in Sierra and had an issue with these controllers and large newer SATA3 drives... Since I'm running an 'unsupported' OS thanks to an unofficial 5,1 update, I can't really complain.

Apparently formatting these in MBR mode as opposed to GPT will also work, as I use them in RAID mode I need to research if I can get the RAID Assistant to do that, but it sounds to simplistic to work...

Lastly, yesterday I had another nasty surprise when I booted into my Windows BOOTCAMP for the first time since changing the drives - BSOD on boot until I entered safe mode and disabled these drives on Device Manager, which I'm fine with as these are HFS+ RAID volumes and can't be easily accessed on Windows. I will try a fresh new Windows UEFI (so non-BOOTCAMP) installation next and see what happens - will post results.

After installing windows UEFI these drives now work in Windows and do not disappear after a reboot. Also when doing a warm boot from Windows back to macOS the drives are fine. The only problem occurs when doing a warm boot from macOS back to macOS - even pausing on the boot menu and reselecting macOS will not solve the problem. This now leads me to believe it's a driver issue (on the maxOS side)...

Will write a more detailed post about my windows installation and findings.

You do have a point, but I'm still finding it hard to swallow for the following reasons:

1. During a warm boot from windows (with the macOS set as default - so not stopping at the Alt/Option menu to select macOS) the drives work
2. During a warm boot from macOS to macOS, but stopping at the Alt/Option boot menu for while (2-3 minutes) still causes the drives to disappear from macOS

In the 1st case above you could argue that Windows will shutdown the drives before macOS in its shutdown sequence and therefore the drives have more time before they are called upon by macOS... but then why wouldn't waiting a few minutes at the boot menu solve this before booting into macOS? I've also read in a few places (herefor example) of people trying to use utilities (such as TinkerTool/Cocktail) to delay system restarts so that the drive has time to spin up, but it didn't work.

If this really is the problem then we're doomed as apple no longer support their older machines that allowed you to plug in any HD (Mac Pros 5,1 and below) so they wont care about fixing it (especially if the cost is slower booting times for their newer machines)... I'm still hopeful that it's a buggy SATA controller driver that may eventually get fixed in a future system update, but given that people seem to be complaining about this for over a year this is probably wishful thinking n my part...

A real pity this... I may begin shifting my work load to Windows as it's running better in my machine than macOS...

I've seen this explanation before, but frankly I don't buy it. I think that if this was the case the problem would be constant (both in a cold boot and a a warm reboot). I've always had two big HDD and one SSD for boot and never had a problem with the recent versions macOS X until I changed to these newer 4TB drives.

As promised I'm posting my results after installing Windows UEFI (build 1803) - which are very interesting.

After installing Windows 10 x64 Pro edition (build 1803) with all other drives removed from my machine, I then proceeded to re insert the drives and to my astonishment no BSOD on boot. In fact both drives show up on Disk Management as normal and healthy and CONTINUED showing up after subsequent reboots (warm boots).

I then installed the bootcamp drivers and during my next reboot I got a BSOD, disabling the HDDs or bootcamp on start up corrects this instability.

The BSOD error I was getting was "CACHE MANAGER" and upon further research I understood that something was attempting to access these disks in an incorrect way and that was causing havoc with CACHE MANAGER, so since disabling bootcamp fixed the instability I concluded that bootcamp was the culprit.

Then I had the idea of properly mounting these drives on windows and found out that Mediafour's MacDrive 10 is capable of doing that (they are Mac RAID volumes).

And it WORKED! Once mounted via MacDrive Bootcamp no longer does whatever it was attempting to do and no more BSOD!

So finally back to my original question - now these drives ONLY disappear after a warm boot from macOS to macOS! Windows to Windows they work fine! Windows to macOS and vice versa also fine!

I'm now thinking that the problem lies in the macOS shutdown, I think the macOS driver leaves these disk in some sort of state that if the power isn't cycled the macOS won't recognize then on start up...

I'm quite surprised, never thought I'd see the day when Windows works better than macOS on a MAC PRO...