As stated by many Web sites, SSL certificates can disappear from IIS when the private key is missing in the certificate store. What’s not mentioned is that oftentimes this is a result of incorrectly created and completed certificate requests. Before you start down a more complicated road, check the easy stuff to eliminate the possibility of errors.
If your security certificate disappears as soon as you refresh IIS, try recreating a new certificate. Erase any old CSR text files and check the creation date to make sure that you are uploading the correct CSR. When the certificate is issued by the certificate authority, make sure you complete the certificate request using the correct file.