Why I am getting a warning when deleting a root CA certificate?

IE displays a warning message when you try to delete a root CA certificate, because it helps preventing you accidently deleting any certificates. After deleting a root CA certificate, all certificates issued by this CA directly or indirectly will become invalid.

If are you sure that you want to delete the selected root CA certificate, you can click the "Yes" button to continue as shown in this tutorial:

1. Start IE as an administrator.

2. Start "Certificate Manager" in IE.

3. Click "Trusted Root Certificate Authorities" tab. You see the list of trusted CA certificates showing up.

4. Scroll down in the list and select "GeoTrust Global CA".

5. Click the "Remove" button. You see the warning message box. It says:

Deleting system root certificates might prevent some Windows 
components form working properly. The list of system critical root
certificates can be reviewed at http://support.microsoft.com/?
id=293781. If Updated Root Certificates is installed, any deleted
third-party root certificates will be restored automatically, but
the system root certificates will not. Do you want to delete the 
selected certificates?

6. Click "Yes" to continue. "GeoTrust Global CA" certificate will be removed from IE. You can import it back later, if needed.

The picture below shows you the delete root CA certificate warning message:

⇒ Import Root CA Certificate into IE

⇐ Start IE as Administrator to Delete Certificate

⇑ Managing Certificates in IE (Internet Explorer)

⇑⇑ Internet Explorer (IE) Certificates Tutorials