We are using Github Organization Folder (via github-branch-source-plugin) + basic-branch-build-strategies.

 

When a PR gets merged in, it is still active in Jenkins. Merged in PRs or deleted PRs/branches should be removed. This might be an issue with the basic-branch-build-strategies plugin?

 

Our current "Orphaned Item Strategy" looks like this:

Re-scanning the organization has no effect unfortunately.