I upgraded to the latest version and some Jobs are missing. No idea why this is happening.
In the log I see the following for every job that is missing:

SEVERE: Failed Loading job BlockCrusher
java.lang.NullPointerException
at org.jenkinsci.lib.envinject.service.EnvVarsResolver.gatherEnvVarsNodeProperties(EnvVarsResolver.java:113)
at org.jenkinsci.lib.envinject.service.EnvVarsResolver.getDefaultEnvVarsJob(EnvVarsResolver.java:87)
at org.jenkinsci.lib.envinject.service.EnvVarsResolver.getPollingEnvVars(EnvVarsResolver.java:41)
at org.jenkinsci.plugins.fstrigger.triggers.FolderContentTrigger.start(FolderContentTrigger.java:371)
at org.jenkinsci.lib.xtrigger.AbstractTrigger.start(AbstractTrigger.java:97)
at org.jenkinsci.lib.xtrigger.AbstractTrigger.start(AbstractTrigger.java:26)
at hudson.model.AbstractProject.onLoad(AbstractProject.java:289)
at hudson.model.Project.onLoad(Project.java:88)
at hudson.model.Items.load(Items.java:115)
at jenkins.model.Jenkins$16.run(Jenkins.java:2484)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:146)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:259)
at jenkins.model.Jenkins$7.runTask(Jenkins.java:874)
at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:187)
at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:94)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)