After Jenkins restart I can build a project/branch/PR exactly once. After that I can see:

INFO: sample-jenkins-pipeline-2/jisr.documentation/experimenting-with-testing-with-Jenkins #1 completed: ABORTED
Oct 12, 2018 11:08:31 AM hudson.model.listeners.RunListener report
WARNING: RunListener failed
java.lang.IllegalStateException: closed
{{ at okio.RealBufferedSink.writeUtf8(RealBufferedSink.java:56)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.get(DiskLruCache.java:433)}}
{{ at com.squareup.okhttp.Cache.get(Cache.java:184)}}
{{ at com.squareup.okhttp.Cache$1.get(Cache.java:139)}}
{{ at com.squareup.okhttp.internal.http.HttpEngine.sendRequest(HttpEngine.java:207)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.execute(HttpURLConnectionImpl.java:450)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.getResponse(HttpURLConnectionImpl.java:399)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.getHeaders(HttpURLConnectionImpl.java:155)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.getHeaderField(HttpURLConnectionImpl.java:199)}}
{{ at com.squareup.okhttp.internal.huc.DelegatingHttpsURLConnection.getHeaderField(DelegatingHttpsURLConnection.java:190)}}
{{ at com.squareup.okhttp.internal.huc.HttpsURLConnectionImpl.getHeaderField(HttpsURLConnectionImpl.java:25)}}
{{ at org.kohsuke.github.Requester.noteRateLimit(Requester.java:350)}}
{{ at org.kohsuke.github.Requester._to(Requester.java:300)}}
{{ at org.kohsuke.github.Requester.to(Requester.java:239)}}
{{ at org.kohsuke.github.GitHub.getRepository(GitHub.java:474)}}
{{ at org.jenkinsci.plugins.github_branch_source.GitHubBuildStatusNotification.lookUpRepo(GitHubBuildStatusNotification.java:146)}}
{{ at org.jenkinsci.plugins.github_branch_source.GitHubBuildStatusNotification.createBuildCommitStatus(GitHubBuildStatusNotification.java:79)}}
{{ at org.jenkinsci.plugins.github_branch_source.GitHubBuildStatusNotification.access$400(GitHubBuildStatusNotification.java:68)}}
{{ at org.jenkinsci.plugins.github_branch_source.GitHubBuildStatusNotification$JobCompletedListener.onCompleted(GitHubBuildStatusNotification.java:306)}}
{{ at hudson.model.listeners.RunListener.fireCompleted(RunListener.java:211)}}
{{ at org.jenkinsci.plugins.workflow.job.WorkflowRun.finish(WorkflowRun.java:807)}}
{{ at org.jenkinsci.plugins.workflow.job.WorkflowRun.access$1100(WorkflowRun.java:143)}}
{{ at org.jenkinsci.plugins.workflow.job.WorkflowRun$GraphL.onNewHead(WorkflowRun.java:1220)}}
{{ at org.jenkinsci.plugins.workflow.cps.CpsFlowExecution.notifyListeners(CpsFlowExecution.java:1437)}}
{{ at org.jenkinsci.plugins.workflow.cps.CpsThreadGroup$3.run(CpsThreadGroup.java:417)}}
{{ at org.jenkinsci.plugins.workflow.cps.CpsVmExecutorService$1.run(CpsVmExecutorService.java:35)}}
{{ at hudson.remoting.SingleLaneExecutorService$1.run(SingleLaneExecutorService.java:131)}}
{{ at jenkins.util.ContextResettingExecutorService$1.run(ContextResettingExecutorService.java:28)}}
{{ at jenkins.security.ImpersonatingExecutorService$1.run(ImpersonatingExecutorService.java:59)}}
{{ at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)}}
{{ at java.util.concurrent.FutureTask.run(Unknown Source)}}
{{ at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)}}
{{ at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)}}
{{ at java.lang.Thread.run(Unknown Source)}}Oct 12, 2018 11:08:32 AM jenkins.scm.api.SCMHeadEvent$DispatcherImpl log
WARNING: SCMEventListener.onSCMHeadEvent(SCMHeadEvent) jenkins.branch.MultiBranchProject$SCMEventListenerImpl@1ceef7f propagated an exception
java.lang.IllegalStateException: closed
{{ at okio.RealBufferedSink.writeUtf8(RealBufferedSink.java:56)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.get(DiskLruCache.java:433)}}
{{ at com.squareup.okhttp.Cache.get(Cache.java:184)}}
{{ at com.squareup.okhttp.Cache$1.get(Cache.java:139)}}
{{ at com.squareup.okhttp.internal.http.HttpEngine.sendRequest(HttpEngine.java:207)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.execute(HttpURLConnectionImpl.java:450)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.getResponse(HttpURLConnectionImpl.java:399)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.getHeaders(HttpURLConnectionImpl.java:155)}}
{{ at com.squareup.okhttp.internal.huc.HttpURLConnectionImpl.getHeaderField(HttpURLConnectionImpl.java:199)}}
{{ at com.squareup.okhttp.internal.huc.DelegatingHttpsURLConnection.getHeaderField(DelegatingHttpsURLConnection.java:190)}}
{{ at com.squareup.okhttp.internal.huc.HttpsURLConnectionImpl.getHeaderField(HttpsURLConnectionImpl.java:25)}}
{{ at org.kohsuke.github.Requester.noteRateLimit(Requester.java:350)}}
{{ at org.kohsuke.github.Requester._to(Requester.java:300)}}
{{ at org.kohsuke.github.Requester.to(Requester.java:239)}}
{{ at org.kohsuke.github.GitHub.getRepository(GitHub.java:474)}}
{{ at org.jenkinsci.plugins.github_branch_source.GitHubSCMSource.retrieve(GitHubSCMSource.java:878)}}
{{ at jenkins.scm.api.SCMSource._retrieve(SCMSource.java:374)}}
{{ at jenkins.scm.api.SCMSource.fetch(SCMSource.java:328)}}
{{ at jenkins.branch.MultiBranchProject$SCMEventListenerImpl.processHeadUpdate(MultiBranchProject.java:1589)}}
{{ at jenkins.branch.MultiBranchProject$SCMEventListenerImpl.onSCMHeadEvent(MultiBranchProject.java:1190)}}
{{ at jenkins.scm.api.SCMHeadEvent$DispatcherImpl.fire(SCMHeadEvent.java:247)}}
{{ at jenkins.scm.api.SCMHeadEvent$DispatcherImpl.fire(SCMHeadEvent.java:230)}}
{{ at jenkins.scm.api.SCMEvent$Dispatcher.run(SCMEvent.java:481)}}
{{ at jenkins.security.ImpersonatingScheduledExecutorService$1.run(ImpersonatingScheduledExecutorService.java:58)}}
{{ at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)}}
{{ at java.util.concurrent.FutureTask.run(Unknown Source)}}
{{ at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(Unknown Source)}}
{{ at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)}}
{{ at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)}}
{{ at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)}}
{{ at java.lang.Thread.run(Unknown Source)}}Oct 12, 2018 11:19:00 AM hudson.init.impl.InstallUncaughtExceptionHandler$DefaultUncaughtExceptionHandler uncaughtException
SEVERE: A thread (OkHttp DiskLruCache/1443) died unexpectedly due to an uncaught exception, this may leave your Jenkins in a bad way and is usually indicative of a bug in the code.
java.lang.RuntimeException: java.io.IOException: failed to rename C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal to C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal.bkp
{{ at com.squareup.okhttp.internal.DiskLruCache$1.run(DiskLruCache.java:181)}}
{{ at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)}}
{{ at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)}}
{{ at java.lang.Thread.run(Unknown Source)}}
Caused by: java.io.IOException: failed to rename C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal to C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal.bkp
{{ at com.squareup.okhttp.internal.io.FileSystem$1.rename(FileSystem.java:85)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.rebuildJournal(DiskLruCache.java:407)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.access$400(DiskLruCache.java:88)}}
{{ at com.squareup.okhttp.internal.DiskLruCache$1.run(DiskLruCache.java:177)}}
{{ ... 3 more}}Oct 12, 2018 11:19:00 AM com.squareup.okhttp.internal.Platform$JdkWithJettyBootPlatform getSelectedProtocol
INFO: ALPN callback dropped: SPDY and HTTP/2 are disabled. Is alpn-boot on the boot class path?
Oct 12, 2018 11:19:00 AM jenkins.branch.OrganizationFolder$OrganizationScan run
INFO: CSD organization #20181012.111900 organization scan action completed: FAILURE in 0.14 sec
Oct 12, 2018 11:20:00 AM jenkins.branch.OrganizationFolder$OrganizationScan run
INFO: sample-jenkins-pipeline-2 #20181012.112000 organization scan action completed: FAILURE in 11 ms
Oct 12, 2018 11:31:00 AM hudson.init.impl.InstallUncaughtExceptionHandler$DefaultUncaughtExceptionHandler uncaughtException
SEVERE: A thread (OkHttp DiskLruCache/1563) died unexpectedly due to an uncaught exception, this may leave your Jenkins in a bad way and is usually indicative of a bug in the code.
java.lang.RuntimeException: java.io.IOException: failed to rename C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal to C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal.bkp
{{ at com.squareup.okhttp.internal.DiskLruCache$1.run(DiskLruCache.java:181)}}
{{ at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)}}
{{ at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)}}
{{ at java.lang.Thread.run(Unknown Source)}}
Caused by: java.io.IOException: failed to rename C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal to C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal.bkp
{{ at com.squareup.okhttp.internal.io.FileSystem$1.rename(FileSystem.java:85)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.rebuildJournal(DiskLruCache.java:407)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.access$400(DiskLruCache.java:88)}}
{{ at com.squareup.okhttp.internal.DiskLruCache$1.run(DiskLruCache.java:177)}}
{{ ... 3 more}}Oct 12, 2018 11:31:00 AM com.squareup.okhttp.internal.Platform$JdkWithJettyBootPlatform getSelectedProtocol
INFO: ALPN callback dropped: SPDY and HTTP/2 are disabled. Is alpn-boot on the boot class path?
Oct 12, 2018 11:31:00 AM jenkins.branch.OrganizationFolder$OrganizationScan run
INFO: CSD organization #20181012.113100 organization scan action completed: FAILURE in 0.16 sec
Oct 12, 2018 11:32:00 AM jenkins.branch.OrganizationFolder$OrganizationScan run
INFO: sample-jenkins-pipeline-2 #20181012.113200 organization scan action completed: FAILURE in 18 ms
Oct 12, 2018 11:38:25 AM hudson.model.AsyncPeriodicWork$1 run
INFO: Started Gravatar periodic lookup
Oct 12, 2018 11:38:25 AM hudson.model.AsyncPeriodicWork$1 run
INFO: Finished Gravatar periodic lookup. 1 ms
Oct 12, 2018 11:43:00 AM hudson.init.impl.InstallUncaughtExceptionHandler$DefaultUncaughtExceptionHandler uncaughtException
SEVERE: A thread (OkHttp DiskLruCache/1693) died unexpectedly due to an uncaught exception, this may leave your Jenkins in a bad way and is usually indicative of a bug in the code.
java.lang.RuntimeException: java.io.IOException: failed to rename C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal to C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal.bkp
{{ at com.squareup.okhttp.internal.DiskLruCache$1.run(DiskLruCache.java:181)}}
{{ at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)}}
{{ at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)}}
{{ at java.lang.Thread.run(Unknown Source)}}
Caused by: java.io.IOException: failed to rename C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal to C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache\D06sSK4O0xohU7Y5_vBnnFPSVeKSfbwBwHAxbgK0kH0\journal.bkp
{{ at com.squareup.okhttp.internal.io.FileSystem$1.rename(FileSystem.java:85)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.rebuildJournal(DiskLruCache.java:407)}}
{{ at com.squareup.okhttp.internal.DiskLruCache.access$400(DiskLruCache.java:88)}}
{{ at com.squareup.okhttp.internal.DiskLruCache$1.run(DiskLruCache.java:177)}}
{{ ... 3 more}}

Removing temp directory C:\Jenkins\org.jenkinsci.plugins.github_branch_source.GitHubSCMProbe.cache helps so that I can build again, but again - only once