If you have problems with the Qualys extension be it you want to install or re-install, do the following


https://community.qualys.com/docs/DOC-5823-deploying-qualys-cloud-agents-from-microsoft-azure-security-center


Found lower in the comments:


Stephen Im Employee Aug 28, 2018 6:03 PM

If you see that Cloud Agents are installed on multiple virtual machines instead of the selected ones in your Azure environment, please set "Auto Deploy" option to of per security solution.

(Home > Security Center - Security solutions > (solution name) > Configure security solution)