The following is the reproducing steps.

1. Create a GitHub organization folder
2. Delete the folder
3. Delete the org's webhook on GitHub
4. Create the GitHub organization folder again
-> Webhook is not registered on GitHub

It is because the existence of webhook is managed on Jenkins master as a file.

https://github.com/jenkinsci/github-branch-source-plugin/blob/github-branch-source-2.0.1/src/main/java/org/jenkinsci/plugins/github_branch_source/GitHubOrgWebHook.java#L104

But I think it is not good idea. It seems that the existence of webhook can be checked by looking at urls of org's webhook.