Just created a whole load of jobs in a Folder.
Did a mass change inside the config files manually ( using a script )
Reloaded config ManageJenkins->reload configuration from disc

Jenkins updated, jobs inside folders were not updated
I'll go for the above...
*Jenkins Version 2.219 *
( tried it on an earlier version, thought I had done something wrong, only a few jobs so changed using Jenkins GUI .. and ignored it.)
All latest plugins installed

Raised it to Major
I have many jobs in folders and changing e.g. the clearcase branch in 20+ jobs using the Jenkins GUI is not amusing when a perl one liner does it almost instantly.

got caught by this again - now I have more folders and jobs.
A one line perl changes all config.xml files, expected a reload config from disk to work.
Jenkins is constantly running jobs, a new restart is not possible.
A reload config allows the jobs to continue.
( does not - my mistake, no downstream job were started, really blown my CI system )
Does raising it to critical put more emphasis on this defect ?
using Jenkins LTS 2.235.5
all plugins are up to date.

Hi, I faced same issue. I need to update job and folders config.xml files manually and then get changes reflected in Jenkins. jenkins-cli reload-configuration was not working for jobs under folders. and "Reload Configuration from Disk" (in UI) was also not working.

TEMP SOLUTION (which worked for me):

create file: reload-configuration.groovy with content

_{import jenkins.model.Jenkins;}

_{import hudson.model.AbstractItem;}

_{import java.io.InputStream;
import java.io.FileInputStream
import java.io.File;
import javax.xml.transform.stream.StreamSource;}

_{Jenkins.instance.getAllItems(AbstractItem.class).each{job ->
  def configXMLFile = job.getConfigFile();
  def file = configXMLFile.getFile();}

  _{if (file.exists()) {}

    _{InputStream is = new FileInputStream(file);}

    _{job.updateByXml(new StreamSource(is));
    job.save();}

    _{println("Config reloaded: " + job.fullName);
  }
}}

And then run it with (add your auth method if needed): 

_{java -jar jenkins-cli.jar -s https://${JENKINS_ADDRESS}/ groovy = < reload-configuration.groovy}

This script goes through all items (jobs/folders) and updates their configs.

Please let me know if something is not clear in this explanation.

Same problem here. Need this fixed, big time.

Vitalii, your solution worked great, thank you.