I found in my friend's eprints, there are many error messages in error.log that say that the file is not found.

While if viewed in the item summary page, the file display is still there, but when clicked, a message appears: 

EPrints System Error. 

Error in file retrieval: failed to get file contents

Then I tried to investigate by looking at the directory where the file from the item is stored. For example:
Item ID: http://repo.domain/2075
File:
1. http://repo.domain/2075/2/Article.pdf
2. http://repo.domain/2075/3/Sample.pdf

When I access the directory,
agung@server:~/archives/testing/documents/disk0/00/00$ cd 20/

only the following directories appear:
10/ 30/ 36/ 41/ 45/ 55/ 58/ 60/ 65/ 68/ 70/ 72/

It turns out that the directory with the name 75/ is not on the list. So the database still lists ID 2075 and the page is still opened, but when I click on the file, all the contents of the file are not found.

Does anyone know why this can happen? because if the file is deleted using the editor or admin user, then the file should not appear on the summary page on ID 2075.

How do you know if this is due to user error or there is a process on the server that suddenly deleted files from its directory.