CircleCI Cloud’s GitHub Enterprise Server Preview attaches one CircleCI organization to one GitHub Enterprise Server organization. This is Cloud plus a GHES hostname. It is not a CircleCI Server install.
A second GHES organization will not list its repositories on a CircleCI organization that is already attached to a different GHES organization. An empty project list in the UI or in Terraform, when you expected the other GHES org, means you are looking at the CircleCI org bound to the first GHES org. The GitHub App install on the first org can be healthy.
Add the other GHES organization
Create a second CircleCI organization.
Install the GitHub App on the second GHES organization and finish setup against that new CircleCI organization.
Keep projects, contexts, and env vars on the CircleCI org that matches that GHES org. They do not move across when you look at the other org’s project list.
GitHub.com organizations and github_app on github.com are a different integration. An empty list there is not evidence that the GHES App install failed.
CircleCI Server customers who run GHES beside Server follow Server’s own GitHub Enterprise setup. This one-org mapping is the Preview product on CircleCI Cloud. The older note that all GHES use requires CircleCI Server does not describe Preview. See Using CircleCI with GitHub Enterprise for the Server path.