Solved Windows EFI Partition mixing up boot?

Hey guys,

I hope you can help me with this - let me first say that I just built my first PC (previously I only had already built systems that my siblings gave me after they got a new one) and I might not understand all the terms, so be patient when I have to ask for an explanation (also English is not my native language, so I'm sorry for any spelling mistakes or weird grammar).

Here's the important data first:
OS: Windows 11 Pro 22H2 - Build 22621.1702
MoBo: ROG STRIX Z790-F GAMING WIFI
Processor: 13th Gen i9-13900K

My problem is the following:
I have just switched PCs and built the new one myself. Previously I used a Samsung 970 Pro as the SSD from which I booted Windows in the old PC.
But in my new system I have one 2TB 990 Pro (which I want to use as my Windows system SSD) and two 1TB 990 Pro's for storage (for files that are currently on external SSDs/HDDs).

So far so good. After I built everything I tried to install Windows 11 from a installation media USB stick.
I installed a fresh Windows 11 install on the 2TB SSD. Worked perfectly. After that I formatted the old Windows install on the 970 Pro (because I want to use that SSD for storage too). Until here everything should've worked out normally.

Here's what my BIOS says - just to make the SSD situation clearer:


And now my problem:
When I start my PC the boot menu shows my old 970 Pro (M.2_2) as the only Windows boot option. But the drive doesn't even have a Windows installation anymore.
Its just unallocated space since I formatted the SSD. When I then click on it to boot it boots the fresh Windows install that I have on my 990 Pro (M.2_1):


After I checked Disk Management I realized that the old 970 Pro did not format completely - there is still a 100 MB partition called EFI on there that I cannot remove via Disk Management - its everything in the right klick menu is greyed out. I guess that's the reason why my BIOS shows this SSD as a bootable drive?


I know it's a lot of drives - I have some old family photos on each of them - the plan is to put everything on one drive and use the others for other projects.
For now I just chucked them all in:


That's where I have a few questions (sorry if they're dumb):
- Did the formatting not remove that EFI partition because its a system partition?
- And if that partition is responsible for the boot of the OS, why did the fresh Windows install not create the same partition on the new 2TB 990 Pro?
- Also - and that's the thing that puzzles me the most: why does the correct Windows (from the 990) boot when I click on the 970 in the BIOS?

What I've already tried:
After googling a bit I've tried to remove the EFI partition on the old SSD with the CMD prompt as Admin.
Because I could not find a way in Disk Management.

But when I tried it via CMD I got the error message: "The selected volume or partition is in use.
To continue with the operation use the OVERRIDE parameter."
Now I'm not sure if I should override it while it is in use.

Maybe some of you can help me understand what the EFI partition does and why it's on my old drive instead of the new one.
Thanks in advance

Oh, I also tried the obvious first step: removing the old 970 Pro drive and only leaving in the new Windows install on the 990 Pro.
But then I can't boot into Windows at all.

The reason your partitions are not built correctly is because you had all your drives connected during the install. Window installs this essential partition on the first drive it SEES during the install process which is not necessarily your system drive where it belongs. This is the reason disconnecting all other drives is necessary during an install to make sure all your partitioning is correct and this partition ends up on your system drive.
This is what you should see per MICROSOFT
The default partition layout for UEFI-based PCs is: a system partition, an MSR, a Windows partition, and a recovery tools partition.


This layout lets you use Windows BitLocker Drive Encryption through both Windows and through the Windows Recovery Environment.

You can always change your boot order in bios pointing it to the 970, but this is a bandaid to allow you to boot with the partition setup you have. It doesn't make your partitioning correct.

I believe your issue can be solved using diskpart from you installation media. But this is over my head. Take a look at @KYHI post here but whatever you do image your drive first. Moving / recreating EFI partition - Windows 10 Help Forums

Personally if it were me, I would play it safe and go the long route.
I would image my system drive, disconnect all other drives, do a clean install which creates all the partitions correctly. I would then restore only the C: partition from my image to the C: partition the clean install created. If the system does not boot, the imaging app I use can fix boot problems. One can also rebuild BCD using the command line from the installation media. Only after Windows boots correctly would I connect other drives.

diskpart
select vol c
shrink desired=100
create part EFI
format fs=fat32
assign letter=s
exit
bcdboot C:\Windows /s S: /f UEFI
diskpart
select vol s
remove
exit
exit

Then what happens when the recovery partition needs to be bigger. Perhaps the op doesnt need one at all.

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Glasskuter gave you the explanation and NavyLCDR gave you the instructions on how to fix it, creating on drive 0 a EFI partition and loading the boot manger on it. Then you will be able to boot from the created EFI partition and delete the EFI partition on drive 2.
If you want to have the Recovery environment on the Recovery partition you should make it bigger (1G) able to install new WinRE or you can move the Recovery environment to C: with the CMD reagentc /disable.


Your mistake was to install Windows with another boot able drive attached and it has installed the boot manager on the EFI partition of the old drive and the OS on the new drive.

Thank you so much for your answers guys!
Then I will first try Glasskuter's suggestion and do a clean install with just the main drive.
I did not know that leaving in other drives could mess up the installation that much, especially since you could specify which drive you want to install Windows to.

I don't really need to make an image of my drive since it was a fresh install.
There are no important files on the 2TB drive anyway.

That is the best solution.
When done don't forget to enlarge the Recovery partition to 1 G. There are many ways to do it.
Best way is to disable the recovery partition environment with the CMD reagentc /disable, enlarge the recovery partition with MiniToll partition and enable recovery partition environment with the CMD reagentc /enable.
The MS solution is a little more complicated

You don't need a recovery partition.

You DO need to create an EFI partition as per NavyLCDR -- but before that you need to "convert the disk to GPT"

You can convert a disk to gpt from MBR without losing data -- in Diskpart just select disk xxxx where xxxx is your C disk, convert GPT and then follow the instructions to install the bootloader.

Cheers
jimbo

A tidbit to know. I have been doing this a long time and discovered this recently in a MS article I came across. Had I known it, I could have saved myself a lot of time in the past. A lot of machines these days have motherboard where one has to remove other components to get to other m.2 drives. This article said instead of physically removing those drives, one can disable the drive in bios before installing, then enable it afterwards. By doing so, the installation process does not see the other drive.
I've not had a need to test this theory yet but it makes sense.

glasskuter said:

A tidbit to know. I have been doing this a long time and discovered this recently in a MS article I came across. Had I known it, I could have saved myself a lot of time in the past. A lot of machines these days have motherboard where one has to remove other components to get to other m.2 drives. This article said instead of physically removing those drives, one can disable the drive in bios before installing, then enable it afterwards. By doing so, the installation process does not see the other drive.
I've not had a need to test this theory yet but it makes sense.

Click to expand...

I did this procedure is some computers with multiple SATA drives. I never did it with multi M.2 drives but I suppose you can also do it .

jimbo45 said:

You don't need a recovery partition.

You DO need to create an EFI partition as per NavyLCDR -- but before that you need to "convert the disk to GPT"

You can convert a disk to gpt from MBR without losing data -- in Diskpart just select disk xxxx where xxxx is your C disk, convert GPT and then follow the instructions to install the bootloader.

Cheers
jimbo

Click to expand...

On a clean install there is no need to convert the drive to GPT or create partitions. The installation process does it for you.

Reset BIOS or load defaults.
Set Disk mode to AHCI, not RAID
Select OS mode = UEFI
Disable fast boot and secure boot (you can turn it on after installation)

Windows can be installed in two ways: Legacy-MBR or UEFI-GPT
To install as Legacy-MBR you must boot the installation drive as Legacy
To install as UEFI-GPT you must boot the installation drive as UEFI.

As you have a UEFI BIOS, you should install as UEFI-GPT
Detach any other drives (SATA or Power cable) from the MB.

During POST, press F12(?) to launch the boot menu. You will see two options for the USB drive. USB UEFI (Name) and USB (Name). Select USB UEFI (Name) to install as UEFI-GPT.
Go to install and delete ALL partitions on the main drive till you have one and only one unallocated space and then proceed.
Don't enable updates or connect to the internet during installation.

If you want to use a local account What is "oobe\bypassnro"

jimbo45 said:

You don't need a recovery partition.

You DO need to create an EFI partition as per NavyLCDR -- but before that you need to "convert the disk to GPT"

You can convert a disk to gpt from MBR without losing data -- in Diskpart just select disk xxxx where xxxx is your C disk, convert GPT and then follow the instructions to install the bootloader.

Cheers
jimbo

Click to expand...

Please don't do this.
#1 The disk is already GPT, it does not need to be converted.
#2 Diskpart Convert GPT only works on empty disks, not disks with data on them:

DISKPART> help convert gpt

Converts an empty basic disk with the master boot record (MBR) partition
style into a basic disk with the GUID partition table (GPT) partition
style.

Syntax: CONVERT GPT [NOERR]

NOERR For scripting only. When an error is encountered, DiskPart
continues to process commands as if the error did not occur.
Without the NOERR parameter, an error causes DiskPart to exit
with an error code.

A basic MBR disk must be selected for this operation to succeed.

The required minimum disk size for conversion to GPT is 128MB.

Important:

The disk must be empty to convert it to a GPT disk. Back up your data,
and then delete all partitions or volumes before converting the disk.

Thank you guys so much!

I tried what Glasskuter said and checked if I could disable the m.2 SSDs in the BIOS without removing them.

But for my motherboard apparently you can only disable one port - m.2_4

So I removed all drives except the main one and did a clean install. After that I added the other drives one by one and removed the EFI partition of the old drive (now it worked where previously it wouldn't let me).

What I didn't do was convert to GPT as mentioned by Jimbo45 since according to Diskpart my drive was already GPT and Megahertz advised against it.

I still think when you install Windows on an empty drive (and specify which drive to install on in the 'Custom Installation' setting, then the installer should ignore all other drives

But now that it worked I'm happy, even if it was a bit more work.
Thank you all so much and I'm gonna close this thread.

Thank you for reporting back it is fixed. Your findings about your drive ports prompted me to look at my own in UEFI. I was glad to see Dell lets me disable all of my internal ports if it's ever necessary for me to clean install. It's a shame mobo companies like Asus don't provide their users the same option since they sometimes make it so difficult to get to the drives.

I don't understand the problem with installing Windows with multiple drives connected. I have a desktop with 5 drives installed and all three of my laptop computers have two drives installed. I've never had an issue putting the EFI system partition and Windows installation on the exact drive(s) where I wanted them.