Post-Dual Boot Cleanup – Reclaiming Lost Partition Space After Removing Ubuntu

Post-Dual Boot Cleanup – Reclaiming Lost Partition Space After Removing Ubuntu

Introduction

This isn’t my usual post about vulnerabilities, bug bounty, or web security. This time, it’s something different — a persistent issue I hit after removing Ubuntu from a dual-boot setup. It messed up my partitions, left behind EFI boot entries, and blocked nearly 100 GB of usable space.

After trying several tools and commands (many of which failed), I finally resolved it — so here’s a write-up for anyone facing the same frustrating post-dual-boot cleanup.

The Problem

After removing Ubuntu:

• I still saw Ubuntu entries in my UEFI boot menu
• Disk Management in Windows showed a 1.07 GB System partition, 98 GB of unallocated space, and wouldn’t let me extend the main partition
• diskpart couldn’t delete the partition: Virtual Disk Service error: The operation is not supported by the object.
• Tools like MiniTool Partition Wizard didn’t help
• WSL showed disk usage but wasn’t able to manipulate partitions

The Solution: Using a Live Linux Environment

Since Windows tools couldn’t fix the partition issues, I needed to approach the problem from outside Windows. A Linux live boot environment provides the perfect tools for this job, particularly GParted, which has more powerful partition management capabilities than Windows Disk Management.

For this guide, I used Kali Linux as my live USB distro (because I keep it around for security testing), but this solution will work equally well with Ubuntu Live, GParted Live, or any Linux ISO that includes GParted.

Step-by-Step Fix

1. Disable Secure Boot

Booting into Kali or any unsigned Linux ISO often fails with a “Security Violation” error. To fix that:

• Enter BIOS (usually F2, DEL, or ESC on boot)
• Disable Secure Boot
• Save and exit

2. Create Live USB (I Used Kali)

• I used Rufus with the following options:
  • Partition scheme: GPT
  • Target system: UEFI (non-CSM)
  • File system: FAT32
• You can use Ubuntu, GParted Live, etc., but I used Kali just in case I needed other tools

3. Boot Kali and Open GParted

Once Kali booted:

• Open GParted
• I noticed:
  • A ~1.x GB “System” partition
  • ~98.x GB of unallocated space that couldn’t be used because the system partition was in the way

Windows couldn’t remove that system partition, but GParted could.

4. Delete the System Partition

• Right-clicked the 1.x GB “System” partition
• Selected Delete
• Now I had one large ~100 GB chunk of unallocated space

5. Resize the Existing Partition

• Right-clicked the main (E:) partition
• Selected Resize/Move
• Dragged to use all the available unallocated space
• Set Align to → MiB (recommended)
• Applied changes using the green checkmark

6. Merge in Windows (Disk Management)

• Rebooted into Windows
• Opened Disk Management (diskmgmt.msc)
• The previously unallocated 100 GB was now directly next to my E: drive
• Right-clicked the partition → Extend Volume…
• Merged the space successfully — no tools needed

Conclusion

Post-dual boot cleanup can get tricky when partitions are locked, out of order, or marked as system-reserved — especially when Windows tools refuse to cooperate. The key takeaway here is: sometimes the only way to reclaim your space is from outside Windows.

While I personally used Kali Linux as my live USB (mostly because I keep it around for security testing), you don’t have to. This method works just as well with Ubuntu Live, GParted Live, or any Linux distro that includes GParted.

In the end, combining GParted for surgical cleanup and Windows Disk Management for finishing touches gave me a clean, single-boot setup with all my space back — no formatting, no reinstalls, no stress.

Got a similar mess? Boot live, take control, and reclaim your space.