After a Windows update, the user’s Linux system failed to boot due to a 90-second wait and encountered dependency failures. Investigation revealed that Windows swapped the order of the Linux partition and the recovery partition, leading to the issue. The user resolved the problem by repairing Linux, updating fstab, reinstalling Grub, and using efibootmgr to change the boot order.

As usual, I finished using Windows, clicked on update, and shut down. At that moment, I thought this Windows update was trivial and wouldn’t affect my computer.

But the next second, I switched to the Linux system and noticed something was wrong.

I booted Linux directly from rEFInd, and everything was fine at first until a 90-second wait appeared:

1

After the 90-second countdown ended, I couldn’t boot into the system:

Dependency failed for file system check
Dependency failed for local file system

Then the system entered emergency mode, but the terminal was accessible.

Moreover, Grub also entered rescue mode, indicating there was a problem with the boot process.

I checked the disk partitions and found that the 10GB Recovery partition of Windows had swapped places with the Linux system partition. It was all due to Windows running rampant on my computer.

Repair Linux

It seemed that there was an issue with a certain partition.

I was completely baffled.

The partition labeled E4F3, which had been executing a certain task, turned out to be nonexistent. Then I looked at fstab and found that this E4F3 was supposed to be mounted to /boot/efi. It seemed that this partition was originally my ESP, and I didn’t know what the Windows update did to change the UUID of the ESP.

fstab

After that, I used the device path directly instead of the UUID.

Repair Grub

It seemed that grub.cfg also used UUID to locate the ESP, which caused the problem this time.

A quick fix can be done with two commands. (However, Grub will be added to the first order of UEFI boot.)

$ sudo grub-install

$ sudo grub-mkconfig -p /boot/grub/grub.cfg

Then I used efibootmgr to change the boot order (I used rEFInd):

$ sudo efibootmgr -o 0001,0002,0003...

I really don’t understand why Windows updates have to be so troublesome.