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Perfect triple boot system broke by Ubuntu 17.10 upgrade

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I had a perfectly working system with OS X Sierra, Windows 10 and Ubuntu 17.04 on three separate SSDs. I use Clover UEFI boot loader can get into any of the OS without problem.

The nightmare started when last week I let Ubuntu upgrade from 17.04 to 17.10. I didn't detach the OS X SSD when the upgrade was happening. After restart, I found grub took over and I can only boot to Windows but not OS X.

At first I thought it was just Ubuntu changing the boot disk order, so I went into my BIOS and change the boot order back to the OS X SSD as the first one. It didn't fix the problem. I was still booting into grub. Then I detached my Ubuntu SSD and Windows SSD. It went straight into grub rescue, and gave me "Unkown filesystem" error.

Then I created a Unibeast USB drive for Sierra in hope it can recognize my OS drive. I can boot into Clover with the USB drive, but in the diskutil I found my OS X SSD partition as marked as Linux!?

I don't understand how Ubuntu upgrade would wipe out a completely unrelated disk? Anybody ran into this problem? I am running out of clues now.
 

P1LGRIM

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Moved to Multi Booting.
 
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At first I thought it was just Ubuntu changing the boot disk order, so I went into my BIOS and change the boot order back to the OS X SSD
There is no boot disk order. Add the path to Clover to the boot menu, use efibootmgr from Ubuntu or EasyUEFI for windows, then change the boot order so that Clover is first.
 

Going Bald

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There is no boot disk order. Add the path to Clover to the boot menu, use efibootmgr from Ubuntu or EasyUEFI for windows, then change the boot order so that Clover is first.
Incorrect. If the OS's are on 3 separate drives then there is a drive boot order that matters.
I had a perfectly working system with OS X Sierra, Windows 10 and Ubuntu 17.04 on three separate SSDs. I use Clover UEFI boot loader can get into any of the OS without problem.

The nightmare started when last week I let Ubuntu upgrade from 17.04 to 17.10. I didn't detach the OS X SSD when the upgrade was happening. After restart, I found grub took over and I can only boot to Windows but not OS X.

At first I thought it was just Ubuntu changing the boot disk order, so I went into my BIOS and change the boot order back to the OS X SSD as the first one. It didn't fix the problem. I was still booting into grub. Then I detached my Ubuntu SSD and Windows SSD. It went straight into grub rescue, and gave me "Unkown filesystem" error.

Then I created a Unibeast USB drive for Sierra in hope it can recognize my OS drive. I can boot into Clover with the USB drive, but in the diskutil I found my OS X SSD partition as marked as Linux!?

I don't understand how Ubuntu upgrade would wipe out a completely unrelated disk? Anybody ran into this problem? I am running out of clues now.
Use USB to boot to Mac OS desktop - mount EFI partition - is Grubx64efi boot file folder in the EFI folder? Has the EFI folder Clover installed been completely overwritten or is Clover still there?
Probably what happened is the Ubuntu installer installed grub to the drive that the BIOS identified as the boot drive. Which in this case happened to be your Mac OS drive.
To fix:
1. remove Grub from the Mac OS drive - instructions are on the Ubuntu forum: https://help.ubuntu.com/community/Grub2#Improvements .
2. Re-install Clover to the Mac OS drive.
3. Install Grub to the Ubuntu drive.
 
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Incorrect. If the OS's are on 3 separate drives then there is a drive boot order that matters
No the device paths are a hard drive + a file path. And it is the file that gets booted, not the disk.

From a bootlog where Clover is installed on a Windows NTFS partition (C: drive), no EFI partition involved - just the device path pointing to the clover executable.
Code:
0:862  0:000  - [07]: Volume: PciRoot(0x0)\Pci(0x1F,0x2)\Sata(0x0,0xFFFF,0x0)\HD(5,GPT,EB68A213-7403-4425-A449-AC57BFB3A8BE,0x21F79800,0x744E800)
0:862  0:000          Result of bootcode detection: bootable Windows (vista,win)
0:863  0:000          This is SelfVolume !!
 
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@vulgo @Going Bald thank you for you answer. I have been out for month and just saw them.
I have been trying to remove grub from the mac drive but not quite successful. If I use the usb boot disk to boot from Clover, Clover recognized my mac hard drive as a linux drive and was not able to boot from it.
I read the Grub2 improvement page, but didn't find the instruction to remove. Could you point out the steps please?

Much appreciated!
 
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@vulgo @Going Bald thank you for you answer. I have been out for month and just saw them.
I have been trying to remove grub from the mac drive but not quite successful. If I use the usb boot disk to boot from Clover, Clover recognized my mac hard drive as a linux drive and was not able to boot from it.
I read the Grub2 improvement page, but didn't find the instruction to remove. Could you point out the steps please?

Much appreciated!
Are you installing all these legacy or something? Macs/hacks have bootable partitions, there is no 'mac drive' and grub 2/efi won't wouldn't normally install to an HFS+ and cannot install to an APFS partition. Boot from the USB, press F2 at the Clover boot menu and upload the saved preboot.log from flash drive /efi/clover/misc/preboot.log - then we can see what Clover is detecting as bootable linux.
 
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Don't know what I did, but now I use the USB drive to boot from Clover and see my macOS disk. See pic.
I can get in but if I don't boot from the USB drive. I cannot boot directly from the disk if I picked it from BIOS. It says this is not a bootable disk and went straight into grub rescure.

I remove the Ubuntu folder from my Mac drive's EFI, but that didn't work.

What puzzled me is if upgrading Ubuntu on a separate disk will not be able to write on to my Mac disk, what stores on Mac disk will lead to grub bootloader?
 

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I just ran into this same issue last night. There’s a second .efi file that’s installed by GRUB into the /EFI/BOOT folder that you just have to remove. I’m not near my computer at the moment, but I think the file name starts with an f. Remove that and reboot, and you should be back into Clover as per normal.
 
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