I am logged in as a Jira Administrator, but when I go to Jira Administration > Manage Apps > Refined Configuration > Site Builder I cannot see all the projects. Where do I find them?
The most likely reason for the Service Desk not to show up in the list is that you are not a project administrator on it.
Go to Jira Administration > Projects
Check the Jira Service Desk-project > Project settings
See that you are added as a project administrator on it. If you are not, add yourself to it
Although it is possible to, as a system admin, add yourself to a project, we have opted for this solution. For companies that have a lot of projects and many system administrators, the list can become very long and to have the possibility to limit the list by only showing projects that the system admin is a part of is the reason for this solution.