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Why Are My Files Disappearing After Uploading?

If you’ve uploaded files to your hosting account and they seem to vanish shortly after, you’re not alone — and your account isn’t broken. The most likely explanation is that our automated malware scanner has detected something suspicious in your files and quietly moved them to quarantine.


What Is the Malware Scanner? #

All NivaCity hosting accounts come with an active malware scanner that continuously monitors your files for threats. It works automatically in the background to protect your website and our shared server environment from viruses, webshells, and malicious scripts.

When a file triggers the scanner, it is quarantined (removed) rather than left in place — this is by design, to protect your site immediately.


Why Would a Safe File Get Removed? #

The scanner uses heuristic detection, meaning it looks for code patterns that resemble known malware — not just exact matches. This works well for catching real threats, but it can sometimes flag legitimate files as suspicious. This is called a false positive.

Files that are commonly mistaken for malware include:

  • Custom PHP applications that handle file uploads or build database queries dynamically
  • E-commerce or CMS scripts with payment processing or admin functionality
  • Files with embedded JavaScript that the scanner considers obfuscated
  • Scripts that create directories or write files on the server

Your file isn’t necessarily dangerous — it may just look similar to something that is.


What Can You Do About It? #

If your files keep disappearing and you are confident they are safe, you have two options:

Option 1: Whitelist Your Files #

We can tell the scanner to ignore specific files or directories so they are never quarantined again. This is the recommended approach if you want to keep malware protection active for the rest of your account.

Option 2: Disable the Malware Scanner #

If you manage your own security and prefer to handle it yourself, we can disable the automatic scanner for your account entirely.


Contact Us to Get Help #

To whitelist your files or disable the scanner, simply open a support ticket or reach out to us directly and let us know:

  1. Which files or folders are being removed
  2. Whether you’d like them whitelisted or the scanner disabled

Our team will take care of it for you promptly.

Note: We recommend only requesting whitelisting or disabling the scanner if you are sure your files are from a trusted source and have not been modified by a third party. If you are unsure whether your files are safe, we are happy to take a look for you.


Still not sure what’s happening? Contact Support and we’ll help you figure it out.