File found while using the cmd locate but it was hidden >> Hacked

This issue might be a funny one but too dangerous
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We can locate the file

locate example..

But we cannot see the file or folder by using  ll, ls , vi ,cd cmds..
The amazing fact is there is no log too. But using the hacked file we can easily login with out permission and upload and sown load the files ..
I have sorted this issue by finding the script in the .htacess file and in the index.php, and php.ini file
tough but crazy one