How to Recover CHKDSK Deleted Files Safely?

  author
Written By Nimisha Ramesh  
Anuraag Singh
Approved By Anuraag Singh 
Modified On December 8th, 2025
Reading Time 8 Minutes Reading

Generally, CHKDSK command is run to fix file system errors or bad sectors of the drive, not for deleting any files or data. Unfortunately, sometimes CHKDSK marks corrupted or orphaned files as “lost chains”. Thereafter, changing those data into .chk files or completely deleting them. If you are one of those persons who have faced this problem. Don’t worry, in this guide, we’ll cover the ways on how to recover CHKDSK deleted files that works well for both novice and experts.

Why Does CHKDSK Deletes or Hides Files?

It is very important to understand before recover CHKDSK deleted files, why CHKDSK sometimes moves, hides, or deletes data. When the command is run, it scans the disk and looking for:

  • Damaged file headers
  • File system errors
  • Lost or orphaned file entries
  • Bad sectors
  • Cross-linked files

If identifies corrupt file clusters by the CHKDSK, it may take the following actions:

  • Convert damaged file fragments into .CHK files
  • Move them into FOUND.000 or similar hidden folders
  • Delete corrupted entries from the file table
  • Unlink files from the file system (making them invisible)

These actions help Windows keep the drive stable, but they can cause unexpected data loss, especially when the files are repairable.

#1: Check the FOUND Folder for .CHK Files

The easiest way to recover files deleted by CHKDSK is to search for the FOUND folder created by CHKDSK.

Steps:

  • By click on File Explorer and simply access the root directory of the drive that has been affected (like C:\, D:\, etc).
  • Turn on ViewHidden Items to show all hidden folders.
  • Locate a folder named FOUND.000 (or similar).
  • Within these folders, you will have files that have the .chk extension, these are file fragments saved by CHKDSK.

Try to restore them manually:

  • Rename .chk files to their original file extensions (for example, .jpg, .docx, .mp4).
  • On the other hand, you can open them with appropriate software.

This method works well in cases where file parts are mostly intact. However, if the files are big or scattered, you should consider using a recover CHKDSK deleted files without losing data recovery option. Which is where the next technique comes into play.

#2: How to Recover CHKDSK Deleted Files? – Advanced

Recovering files manually using the previous method is not always successful, in these situations specific software is used to restore data. SysTools Hard Drive Recovery is a professional tool to recover permanently deleted files by CHKDSK from internal or external drives quickly.

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Why Choose this Automated Tool?

Deep Scan Algorithms: This software has the capability to perform in-depth scanning, sector-by-sector analysis of the attached drive searching for deleted, formatted, and corrupted data.

  • Supports All File Types: It retrieves information in any file formats such as documents, photos, videos, and system data whatever file type you want to recover.
  • Preview Before Recovery: Allows you to preview recoverable items before saving it.
  • Supports All Storage Devices: HDD, SSD, USB drive, and SD card
  • Safe & Read-Only Process: Prevents any more harm being done or data overwriting.

Recover CHKDSK Deleted Files By:

  • Downloading & Installing the aforementioned software
  • Run the tool and click on affected drive from the list
  • Depending on the data loss situation, select the Scan or Formatted Scan option, check example below in image.

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  • After the scanning process ends, preview all the files that can be recovered inside the tool.
  • Choose the files to be restored and hit Save to save them a secure drive.

With this technique, you can easily & securely restore CHKDSK deleted files, even if they are fragmented or removed from the file allocation table.

#3: Restore Data from Backup

If you occasionally take backups of your system using the Windows Backup, File History, or other external software, you could be able to restore lost data without any trouble.

Steps:

  • Launch the Control Panel go-to File History or Backup and Restore depending on older/newer systems.
  • Choose Restore personal files.
  • Browse through previous backup versions.
  • Finally, select the files that are deleted and click Restore.

Even though backups are sometimes not up to date, it is nevertheless one of the fastest and safest recovery methods if available.

#4: Use Command Prompt to Reassign File Attributes

This is another uncommon case, where CHKDSK hides or marks files as system protected. Follow this method to make them visible.

Steps:

  • Press Windows + R, type cmd and hit Enter.
  • Run the following command:

attrib -h -r -s /s /d D:\*.*

  • (Replace D: with the letter of your drive).
  • Hit Enter and then let it run through the process.
  • Look for files returned to your drive.

This will unhide all files such as hidden and system. Thus, making them visible again in File Explorer.

Signs That CHKDSK Has Deleted or Moved Your Files

In the process of Recovering CHKDSK Deleted Files you will notice the following If CHKDSK caused data loss as these are strong indicators that CHKDSK reorganized or repaired file entries.

  • Missing folders, photos, or documents
  • New folders named FOUND.000, FOUND.001, etc.
  • Files with .CHK extension
  • The drive showing less available storage even though no files are visible
  • Hidden files or folders
  • When applications is showing “file missing” or “path not found” errors

Important Precautions to Avoid Overwriting

As soon as CHKDSK deletes or hides any file, do not use the corrupted drive any more. This makes the lost data unrecoverable, because any new file written to it may overwrite the lost data. We can try using the best practices for fast & safe recover CHKDSK deleted files as below:

  • If you are planning to recover deleted files I would suggest not installing recovery software on the same drive.
  • Do not save the stored data in the previous location.
  • Disconnect external drives after recovery.

The faster you act, the greater the chances of recovering the lost data completely with the specialized tool.

How to Prevent CHKDSK From Deleting Files?

You can prevent data loss during a CHKDSK scan by following these tips:

  • Create Regular Backups: You can use file history, OneDrive, or any external backup solution.
  • Monitor Disk Health: With using the smart monitoring tools users can detect early disk failures.
  • Avoid Improper Shutdowns: Due to the sudden power loss or crashes it can cause file system corruption.
  • Replace Failing Drives: If your drive makes noise, becomes slow, or shows CHKDSK errors, replace it immediately.

Common Questions Regarding Recover CHKDSK Deleted Files

  1. How do I know if CHKDSK actually deleted my files or just hid them?

Answer: You can check If your files are no longer visible and the drive storage space is not increased in this case we may consider this your file is hidden rather than deleted.

Common signs include an empty FOUND.000 folder, files showing as “System Protected,” or missing items that are still taking up disk space. You can follow steps to recover data from the FOUND.000 folder easily.

Deep recovery tools can analyze the drive at the cluster level that confirms data is still present and can be restored.

  1. Can CHKDSK delete only some files and not the rest?

Answer: Yes, of course. CHKDSK works at the file system layer, not the file layer. It only removes entries, as you can see below:

  • Are stored in damaged sectors
  • Have timestamp inconsistencies
  • Fail file-system verification
  • Are linked to bad directory records
  1. What are orphan file record segments & why are they deleted?

Answer: When the data is still present on the disk called orphan file record segment but here need to understand it is only a metadata such as the name, folder location, or path, is missing or corrupted.

CHKDSK removes these entries because they cannot be safely mapped to the directory structure, they cause errors in the file system tree, and in some cases they can even start a never-ending allocation loop.

Since the file’s identity has been lost, only advanced recovery software can reconstruct the missing metadata and restore the file properly.

  1. What should I do before running CHKDSK to avoid future data loss?

Answer: Before running CHKDSK on any unstable drive, you should:

  • Take a raw image of the drive, if possible.
  • Clone the disk using dd or sector imaging tools.
  • Avoid the “/f” and “/r” switches until they are necessary.
  • Use read-only scan tools first to check the drive’s health.

Many experts suggest never running CHKDSK on a failing hard drive without first imaging it.

  1. Is it safe to delete .CHK files if I no longer need them?

Answer: The simple answer is yes as .CHK files are safe to delete as they are just fragments, leftover chains, or error repair outputs. So deleting them will not harm the system.

Final Thoughts

If you lost some files after running CHKDSK command. Don’t worry, you are not alone as long as you pay attention and act quickly! If recovered data seems missing, firstly open the FOUND folder and apply command-line recovery if the data is simply hidden away. Lastly, recover CHKDSK deleted files with an authentic, safe, and professional recovery.