AtomicFileWriter.commit should use Util.deleteFile so as to get a more meaningful error message in case the deletion fails.
The following is not helpful in terms of diagnosing the root problem:
java.io.IOException: Unable to delete /…/jobs/demo/builds/…/workflow/3.xml
	at hudson.util.AtomicFileWriter.commit(AtomicFileWriter.java:112)
	at hudson.XmlFile.write(XmlFile.java:179)
	at org.jenkinsci.plugins.workflow.support.storage.SimpleXStreamFlowNodeStorage.saveActions(SimpleXStreamFlowNodeStorage.java:106)
	at …