We are still facing the same issue as JENKINS-54126 even with the fix https://github.com/hub4j/github-api/blob/github-api-1.321/src/main/java/org/kohsuke/github/GitHubClient.java#L778.
I cannot find the log “Encountered GitHub invalid cached 404…” in Jenkins log.
 
Infra:
Jenkins core 2.504.2
GitHub Branch Source 1822.v9eec8e5e69e3
 
Reproduce steps: 
1. Open a PR

2. Make sure PR has been indexed on Jenkins

3. Close this PR, Scan repository on Jenkins

4. Reopen this PR, scan repository on Jenkins again  - and see in logs:

Getting remote pull requests...
Checking pull request #2
‘Jenkinsfile’ not found
Does not meet criteria