Since you've run Disk Utility to check your external hard drive and it shows no problem, your drive should be safe from a corrupted file system. It's likely your folders are hidden by the system. All you need to do is to show hidden files on Mac.
How to show hidden files on Mac:
Option 1. Use keyboard combinations.
Step 1. Locate your external HDD under Locations in Finder.
Step 2. Press Command + Shift + Period (.) key shortcuts.
All hidden files and folders will show up. Double-click on them to view the content.
Option 2. Uncover hidden files in Finder
Step 1. On your Mac, launch Finder.
Step 2. Select Go from the menu bar and then press the Option key, you will see the Library folder from the menu list.
Step 3. Click the Library folder to find out if there are any files or folders you are looking for.
Option 3. Show hidden folders with Terminal
Step 1. Launch Terminal. Enter the following commands and hit the Enter key.
defaults write com.apple.finder AppleShowAllFiles TRUE
Step 2. Keep typing the command below to refresh the Finder.
killall Finder
Check the Finder now, can you see all files and folders on Mac?
To avoid this situation happening again, you can check the reasons why files or folders disappear from your external hard drive on Mac:
- Files are deleted by accident.
- The external hard drive is not properly formatted.
- Due to some malware or virus attacks, the folders are missing.
- Files are hidden by the macOS.
- The file system of your external disk is corrupted.