I've asked Qualys many times and I believe there is a feature request opened for this, but I wanted to document the issue in a discussion to see how others handle this issue. I frequently run into situations where "fixing" vulnerabilities usually involves someone turning off the host/service. Because of this, the host doesn't always respond on a re-scan, thus the vulnerabilities and corresponding remediation tickets never get closed. I have asked Qualys years ago to add a scan option in their option profiles to "close issues if host does not respond", but this has not been done. So instead I have go around that:
1) Use the API to close my remediation tickets marking them as Ignored
2) Run TNE to close the internal tickets
3) Purge the hosts
4) Re-launch a scan against the IP.
It would be much easier and make more sense to me if we could have a custom scan profile that allows issues for non-responding hosts to be automatically closed.