Windows Update Deleted Linux! What to Do and How to Prevent It

Christian Cawley 29-10-2018

You’ve been happily using Windows and Ubuntu on the same computer for months, but then a Windows Update is issued—and disaster strikes!


Windows Update has left your Linux partition unreadable. There’s no boot selection screen, and after investigation it appears the Linux partition has been deleted. Here’s what you can do to fix things and ensure this never happens again.

Windows Updates Don’t Care About Linux

Dual booting Windows and Ubuntu (or another Linux distro) gives you the best of both worlds. But it also gives you the worst.

When Microsoft issues an update for Windows 10, it is largely unconcerned with any operating system or software existing beyond the Windows partition (with some exceptions, such as the UEFI, and recovery partition).

Linux partitions use the EXT4 filesystem, as opposed to NTFS. Windows is only concerned with the latter, so data stored in EXT4 formatted partitions is likely to be ignored. Not in a good way.

The result of this is that partitions can be removed, or even overwritten by the Windows Update process.


Lost partitions can usually be dealt with. Overwritten data, meanwhile, is far tougher to deal with. So, what can you do about it?

First, Try to Recover the Partition

If your Linux data is lost, you need to find out if it can be recovered. Several Linux recovery tools The Best Ways To Recover Data On Linux No matter whether it was your fault or not, things can happen to the data stored on your devices. Hard drives, solid state drives, and removable media can all potentially "lose" files because of numerous... Read More are available, ideal for searching the hard disk for data.

Make sure you have sufficient space for recovery, however. The data will need to be recovered to an external drive, or a different partition that predates the data’s deletion.

It may even be possible to reinstate the entire missing Linux partition. If this is the case, you’ll need to repair the bootloader. Our guide on how to fix a Linux PC when it won’t boot How to Fix Your Ubuntu Linux PC When It Won't Boot Although usually reliable, sometimes Ubuntu won't boot. But why is this and how can you repair your PC when Ubuntu won't start? Read More shows you how to do this.


On some occasions, however, recovery and repair isn’t possible. You’ll be stuck without your Linux data, some of which might have been vital. Indeed, Linux might be your primary operating system, with Windows an afterthought, just a guest on your computer.

How to Prevent Windows Updates Deleting Linux

So, the chances of recovering a wrecked Linux partition at the hands of Windows 10 are minimal. So what can you do about it?

1. Make Regular Data Backups

Create a Linux disk image for backupThese days, no one should be running a computer without keeping at least a backup of their vital data.

Personal data can easily be backed up, either to the cloud, or to a local device. This might be an external hard disk drive, or a USB flash stick. For the best in basic backup, however, you should use both, maintaining your personal data in the cloud and making regular local backups. See our roundup of Linux cloud solutions 10 Cloud Solutions You Should Be Using on Linux Some mainstream cloud storage options don't offer a decent Linux client. But you're not out of luck. Many popular services do work under Linux. You can even roll out your own cloud solution! Read More to find compatible services.


More advanced backup options are also available. Backing up your entire disk to another drive is possible. Although disk backup tools are available for Windows, Linux has a full disk cloning utility built in How to Clone Your Linux Hard Drive: 4 Methods Need to clone your Linux hard disk drive or partition? Use one of these drive cloning tools to clone your Linux disk. Read More . They make complete copies of your disk drives, backing up the data to an external drive of the same, or larger size.

You can also use such tools to copy specific chunks of data; e.g., just the operating system and personal data.

2. Install Operating Systems on Separate Hard Drives

One sure fire way of avoiding the loss of Ubuntu thanks to Windows Update is to use two separate drives.

Many people rely on a single hard disk drive, split up into multiple partitions. One of these is used for Windows 10, while the other is reserved for Linux.


This is how so many problems occur with Windows Update messing up Linux. Windows 10 needs the extra space for the update, so the EXT4 partition is deleted, reformatted, and the space used.

However, if you employ separate physical disk drives, this will not happen. The process of dual booting Windows and Ubuntu remains the same, but with one difference: you just need to ensure that Linux is installed on the second disk drive.

To make this work, you’ll need to ensure your PC has separate physical drives. If not, check our tips on how to install a second hard disk drive 5 Things to Consider When You Install a SATA Hard Drive Before you install a SATA hard drive, here are a few things to consider so you don't mess anything up. Read More .

3. Run Windows or Linux in a Virtual Machine

Create a Linux virtual machine in Windows with VMWare

Messing around with dual booting and additional hard disk drives can be as big a pain as attempting to recover lost data. You might prefer a simpler solution that doesn’t require an extra drive.

Virtualization allows you to create a virtual machine—a software version of your computer’s physical hardware—and install an operating system within it. Windows 10 runs well in a virtual machine (VM), as does Ubuntu and other versions of Linux.

How you do this depends on which operating system you prefer to use day-to-day, and which you’re happy to switch to occasionally.

If you want to install Windows in a virtual machine in Linux How to Set Up a Windows Virtual Machine in Linux Many home users prefer to run a dual-boot setup when both Windows and Linux are needed, but if you'd rather run Windows inside Linux, here's how to set that up. Read More , you can. Similarly, it’s also possible to setup a Linux virtual machine in Windows 10 How to Install Linux in Windows With a VMware Virtual Machine Do you want to install Linux, but can't leave Windows? Try a virtual machine to run your favorite version of Linux inside Windows. We show you how to set up VMware Workstation Player. Read More . Both of these options will prevent Windows Update from deleting Linux.

4. Run Linux or Windows From a USB Drive

Not all that bothered about a physical installation of your alternative operating system? Insufficient resources for a virtual machine? Don’t worry. You can run a portable version of your chosen operating system from a USB flash drive.

With a portable Linux operating system that you can load up as and when needed from external media, Windows Update cannot cause problems.

Perhaps the best way of doing this is to run Linux from a USB drive Running Linux From a USB Drive: Are You Doing It Right? Did you know that can do a full install of Linux on a USB drive? Here's how to create a Linux USB PC in your pocket! Read More , as this is more reliable. There is a tool called Windows To Go that will create a portable version of Windows How to Create a Portable Windows To Go USB Drive Carry Windows in your pocket with Windows To Go. We show you how you can run Windows from a USB drive, like a portable app. Read More , but this is currently limited to Enterprise editions of Windows. That means that if you’re using Windows 10 Home, as most people do, Windows To Go won’t work for you.

Don’t Let Windows Update Destroy Linux!

Windows was not designed to run alongside Linux. The fact that it does so, reasonably well, is thanks to the efforts of its designers.

Losing data on Linux due to a Windows Update is frustrating. Often, Windows is merely tolerated, left on a computer as an option for specific apps. It might even be a condition of employment that Windows is used.

Whatever the situation, keep in mind that you can avoid letting Windows Update loose on your Linux partition. Take precautions:

  1. Make regular backups
  2. Install each operating system on a separate physical hard drive
  3. Run your secondary operating system in a virtual machine
  4. Run your secondary operating system from a USB drive

If you need to use Linux alongside Windows 10 and can’t do any of the above, you’re at risk of losing your Linux partition. At the very least, take the time to delay your Windows Updates How (Not) to Upgrade to the Latest Windows 10 Version The Windows 10 October 2018 Update will roll out soon. Whether you want to latest feature upgrade now or wait, we show you how. Read More until you’re able to take precautions.

Image Credit: PicsFive/Depositphotos

Related topics: Disk Partition, Dual Boot, Linux, Troubleshooting, Windows Update.

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  1. Richard Dierolf
    May 24, 2020 at 9:34 am

    Using separate disks doesn't always prevent this from happening, disconnect the disks instead.

  2. John
    November 7, 2018 at 9:15 pm

    I read the article in order to prevent Windows from deleting my Linux distro. What I learned was... don't use Windows? Why didn't you say that in the first sentence?

  3. Somewhat Reticent
    November 4, 2018 at 5:00 am

    The grub2win project at SourceForge simply avoids most such issues altogether, using a procedure unaffected by most such versions/updates.
    Consider: Microsoft Windows is designed to allow for multi-booting with older or alternate versions (or DOS).

  4. Gary Swann
    November 3, 2018 at 4:49 pm

    Ryan, that's a pint I owe you. Not havin' a scroll bar has been doin' my 'ed in. Thank you.

  5. Jim
    October 30, 2018 at 8:28 pm

    My solution was to delete Windoze. It worked great.

  6. Alister Hood
    October 30, 2018 at 8:23 am

    > Linux partitions use the EXT4 filesystem, as opposed to NTFS. Windows is only concerned with the latter, so data stored in EXT4 formatted partitions is likely to be ignored. Not in a good way.
    > The result of this is that partitions can be removed, or even overwritten by the Windows Update process.

    Linux can use all kinds of filesystems, not just EXT4, but Windows doesn't need to understand any of them in order not to delete them without asking. All it needs to understand is the partition table. If Windows is doing this then it is clearly a deliberate choice, and it is also clearly Evil.

    > Windows was not designed to run alongside Linux.
    > The fact that it does so, reasonably well, is thanks to the efforts of its designers.

    So in what respect does it do this "reasonably well"? Only occasionally deleting partitions without asking? Instead of doing it at every boot?
    Seriously, what a load of nonsense. I hope nobody's coming here for tech wisdom.

  7. Al H.
    October 29, 2018 at 7:53 pm

    Windows has always had this problem, and MS doesn't really seem to care.

    The problem shows up on MBR (vs GPT) partitioned disks. Remake your disk at GPT and your risk factor should be zero.

    • Big al
      October 30, 2018 at 3:08 am

      They don't care because I believe this is a plan problem.

  8. Mike Walsh
    October 29, 2018 at 4:31 pm

    Of course, even if you install Linux to a separate hard drive, you still want to make sure that Windoze hasn't got the faintest clue that said hard drive even exists. If it does, it'll still try and appropriate it.

    I'm curious. Many people try to tell me that for Windows 10, even a 500 GB hard drive is on the small side. What the hell does Windoze DO with all that space?

  9. Dave L
    October 29, 2018 at 4:02 pm

    Unfortunately, a separate drive doesn't a sultuon to prevent Windows from altering Windows to not allow Linux to boot.

    Case in point. Afew years ago in my Asus G72 laptop, one drive nay had Windows 8 and one drive bay had Fedora Linux. I removed the Linux drive and did the free Windows 10 update at the time. It updated well. I placed my drive back in the laptop, with Windows in the other bay. Linux no longer shown in BIOS bootloader.

    No problem, I readded the Linux as an option. Still cannot boot.

    So I took out the Windows drive, only have Linux in drive bay two, still will not boot.

    The data was not removed, but I can no longer can use the Linux drive in this laptop.

    After years of research, I just bought a new laptop and run Fedora alone.

    • hmmm
      November 3, 2018 at 8:37 pm

      Nothing to do with what is discussed here, old known problem, windows just erased the boot record (grub) and replaced it by his own. Solution would have been insert a Linux USB and reinstall grub