Strange Issue Dual Booting Windows 10 and Sierra on Two Separate SSD's

[Bionic Beast]

I used to have El Capitan and Windows 8 working on two separate drives perfectly for the most part and have had dual boot working great for years. For some reason after some time I started having strange issues while booting into either OS or having slow loadup speeds when booting onto mac side. So I decided while I had some free time I was going to do a full clean wipe of both the windows and mac ssd and start fresh. To summarize my installation process. Made a windows 10 (rufus GPT) and sierra usb install on two usb drives. Booted into sierra installer, wiped both ssd's with disk utility as Mac os Journaled and GUID, and then installed sierra. I get sierra working fine using Clover UEFI bootloader and I can boot from it without the need for the usb installer (aka clover is working fine) so I begin the windows install. I unplug all drives except the windows ssd and install windows onto that. I make sure I can boot into windows with no issues as well. Now here is where the problem occurs. I plug my drives back in, and my 3tb storage hdd is recognized just fine in windows and clover, however in clover I am not longer able to see my sierra ssd, but I can see the recovery partition for it. So I use the sierra install usb and check in disk utility and it seems like somehow after the windows install, my Sierra partition is being corrupted/wiped because under the ssd name the partition no longer says "Macintosh HD" but is being replaced with just "--" So somehow after the Windows install, the Sierra partition which is on a completely different ssd is being wiped out. I have tried this process 3+ times and the same thing keeps happening. I know I am not wiping the partition because the ssd is unplugged during the windows install. Only when I plug it back in and then try t boot from it or the sierra install usb do I realize that the partition is gone. So I am not sure what in the world could cause this but any input or ideas would be super appreciated because this has already taken up close to 24 hours of time spread across a few days trying to resolve and I am out of ideas and extremely stress because of this. Thank you!

Relevant Specs:
MoBo: GIGABYTE GA-Z87X-UD4H on version F9
Two Samsung 840 EVO SSD's


UPDATE:

Plot twist...

So since I already had windows installed and my sierra partition got removed somehow, I decided to just keep windows on their and install sierra afterwards. Once I did that, the same thing that was happening to sierra was happening to windows. And I cant boot to it via clover or any other method. So i checked and the only difference is the partition name still showed up in Disk Utility but it said that only 300mb of it was being used (it should be gigs of data since the OS was installed on it). So now Sierra works great but windows is borked. For some reason whenever I install one os, the other is getting destroyed and I have absolutely no idea why.

 

[cmn699]

To summarize my installation process. Made a windows 10 (rufus GPT) and sierra usb install on two usb drives. Booted into sierra installer, wiped both ssd's with disk utility as Mac os Journaled and GUID, and then installed sierra. I get sierra working fine using Clover UEFI bootloader and I can boot from it without the need for the usb installer (aka clover is working fine) so I begin the windows install.

Wondering why you had to use the Sierra USB Installer in UEFI mode to get to the Installation screen >Utilities>Disk Utility to erase the Windows SSD when you already have a Windows 10 UEFI USB Installer that can be used to partition its target SSD in GPT scheme and format it in NTFS and install the Windows 10 system just fine.

In my experience with Multi-disk Multi-boot systems, I would create a USB installer of Windows 10 in UEFI mode using Rufus like you did.

I then connect only the SATA HDD or SSD for Windows 10 installation to SATA port #2 ( in SATA Port 0, Sata Port 1 series it will be SATA Port 1) reserving Port #1 (SATA Port 0) for macOSSierra SSD. This is done in advance for Clover containing disk[macOSsierra] to be at the Highest Boot option when all systems are installed.

I would select and configure all BIOS options I would need to install macOSSierra at this time (and those BIOS Options will be perfect for Windows 10 in UEFI mode also).

I will then set the USB UEFI disk as the first boot device and boot to Windows Installation screen. I will choose a New Installation option. Since this is a previously used SSD , I will delete all the partitions and then use the entire free space to start the Windows 10 Installation . Windows Installer will create all the required partitions , format them and install the System.

Post install reboot, system setup including all the drivers and needed applications and Windows Updates will be done and rebooted several times to make sure the newly created Windows 10 system is working OK.

I would then disconnect the Windows 10 SSD to avoid any possible mistakes during the macOSsierra installation such as mistakenly formatting the Windows SSD at the disk utility screen instead of the SSD intended for Mac!

I will boot with Sierra UEFI USB Installer and after partitioning and formatting its target SSD, I would complete the macOSSierra installation followed by Clover EFI bootloader installation, installation of required kexts and System definition as per the GUIDE. Multibeast is my usual first choice for this.

If there are any Mac updates available , I will try to install them as well.

Once I can boot the macOSSierra System without the USB installer, to convince there are no glitches, I try rebooting the System a few times to make sure it boots OK and its Video, Audio, Internet , FaceTime and iMessage are all working OK.

Once that is done , I shut down the Computer and reconnect the disconnected Windows 10 SSD and reboot the Computer.

I will enter the BIOS and make sure macOSSierra System SSD has the highest boot priority. I will also select other disks and then choose the "Disable" option under Boot Menu. Even when there is only macOSSierra SSD in the Boot menu with all other options disabled, Clover can still show "phantom" boot options. Therefore during the boot I will press the Hotkey to get the Boot Menu and select the macOSSierra disk to enter Clover Boot Menu.

To get rid of other unwanted boot options noted in the Boot menu screen, I will use the Clover Shell command option and "bcfg boot dump" command to list the boot options and using bcfg boot rm "0n" ( where "0n" can be numbered items like "05" that are not true HD but pci "ghosts" that can be removed with the "rm" command. True boot devices will have "hd" following the "0n".
After " bcfg boot rm 0n" command , repeat the "bcfg boot dump" command, until all phantom disks are identified and removed and then type "exit" to get back to Clover Boot Manager menu to continue to boot Windows or Mac.

 

[Bionic Beast]

So I have done very similar to the I have sierra in port 0 and windows in port 1. I only wiped windows ssd in disk utility because it was convenient, but I would still format the drive using the iwndows usb install before installing windows on there anyways. Besides those I followed the steps you outlined but I installed sierra first. removed sierra ssd, and inserted windows usb install and formatted windows ssd and installed windows. Both windows and sierra had been rebooted and all updates installed multiple times. Then After windows was up and running I would plug in sierra ssd to find that I could not boot to it anymore, using clover or anything else. I did the same thing but started with windows, made sure it booted fine, unplugged and then installed sierra and made sure all worked and when I plugged windows ssd back in and it was magically wiped somehow as well. Something at a bios/clover level is wiping these drives and formatting them to match the partition style of whatever OS was last installed. If windows was last installed the mac ssd somehow becomes a blank ntfs drive. If sierra was last installed, windows ssd somehow becomes a blank mac os journaled drive. No idea what could be causing it. Like I said I have used this very same setup for years and never had an issue until clover became the only option, and even then I had clover working for about a year and suddenly now it stopped working. Thanks for responding, I might try some of the smaller details you mentioned.

 

[Bionic Beast]

deleted

 

[cmn699]

Make sure Windows Boot- loader (BOOTMGR and Winload.exe) dose not see your macOSSierra's Clover EFI bootloader as a 'new kid in the block" and 'knock the life out of it' as Windows is known to do with any bootloader that stands in its way to keep up its own hegemony over all other Operating systems. That is the most common cause for a perfectly functioning mac or Linux OS in a multiboot system failing to boot, if Windows installation and booting for the first time in a dual boot system follows the other 'healthy OS" that preceded Windows.
If you install Windows 10 First and make the Clover containing Mac as the First boot device to initiate the booting process Windows Boot manager cannot write on and corrupt Clover boot files and both systems can coexist amicably.

 

[Bionic Beast]

So to be safe I just started from scratch, flashed/wiped BIOS, wiped one drive (I actually found out that somehow my previous sierra install that was fully setup somehow got transferred onto my windows ssd, which still leads me to believe that they were somehow wiping each other out which is the weirdest thing I've ever heard of but anyways, I jyst kept that partition unwiped because it was already all setup which took me hours), disabled all but sierra ssd, booted a few times and it worked fine. For windows I remade my install usb on a 8gb usb drive instead of the 128gb I was using in case that was causing any issues. Disabled all drives except windows drive and then installed windows. Got in there installed basic drivers and let it reboot all the times it needed, then went into BIOS and disabled all other boot options except the "Mac OS X" option being boot priority #1. I wanted to see if I could boot windows from clover but I tried all windows options available (a few legacy drives, most likely my 3tb ntfs drive I use for storage, and I also tried the "boot microsoft efi" option) and none worked. But it actually showed me that when you try to boot windows from clover it manually puts itself back at boot priority #1 in BIOS. So once again I set mac osx to be the first and only boot option and that allowed me to get back into clover. So as of now I have both OS's functioning, only minor downside is that I have to manually boot from the windows ssd instead of being able to load it from clover like I can with Sierra. Now I'm sure theres a way to get the windows ssd working from clover (I know because ive done hours of research on how to get it to work and trying to mess with that s most likely got me into this whole situation), but now that I have everything working, I honestly could care less. If I have to click F12 on bootup to get to Windows then so be it.

I changed so many variables during this go around so I'm not sure what helped it finally work if it was one thing or a combination of things but either way, you're advice somehow helped along to getting to the promise land, so for that you have my thanks!

 

[Going Bald]

So to be safe I just started from scratch, flashed/wiped BIOS, wiped one drive (I actually found out that somehow my previous sierra install that was fully setup somehow got transferred onto my windows ssd, which still leads me to believe that they were somehow wiping each other out which is the weirdest thing I've ever heard of but anyways, I jyst kept that partition unwiped because it was already all setup which took me hours), disabled all but sierra ssd, booted a few times and it worked fine. For windows I remade my install usb on a 8gb usb drive instead of the 128gb I was using in case that was causing any issues. Disabled all drives except windows drive and then installed windows. Got in there installed basic drivers and let it reboot all the times it needed, then went into BIOS and disabled all other boot options except the "Mac OS X" option being boot priority #1. I wanted to see if I could boot windows from clover but I tried all windows options available (a few legacy drives, most likely my 3tb ntfs drive I use for storage, and I also tried the "boot microsoft efi" option) and none worked. But it actually showed me that when you try to boot windows from clover it manually puts itself back at boot priority #1 in BIOS. So once again I set mac osx to be the first and only boot option and that allowed me to get back into clover. So as of now I have both OS's functioning, only minor downside is that I have to manually boot from the windows ssd instead of being able to load it from clover like I can with Sierra. Now I'm sure theres a way to get the windows ssd working from clover (I know because ive done hours of research on how to get it to work and trying to mess with that s most likely got me into this whole situation), but now that I have everything working, I honestly could care less. If I have to click F12 on bootup to get to Windows then so be it.

I changed so many variables during this go around so I'm not sure what helped it finally work if it was one thing or a combination of things but either way, you're advice somehow helped along to getting to the promise land, so for that you have my thanks!

See the pinned guide in the Multi Booting forum for instaling EFI on separate drives.