I tried rolling back the FSTrigger plugin to version 0.30 and my jobs are back. So, I guess version 0.31 or 0.32 has introduced a bug.

Please try fstrigger-plugin 0.33 and let me know.

Somehow I only see 0.32 in the Update Center. Is that the correct way or is there any other way where I can get 0.33?

Maybe just a question of time.
Anyway, you are able to download manually the plugin file (hpi file) in the Jenkins maven repository (http://maven.jenkins-ci.org:8081/content/repositories/releases/org/jenkins-ci/plugins/fstrigger/0.33/)
Please let me know.

Version 0.33 does not solve the problem for me. The jobs are missing. The same as in 0.32. So I reverted back to 0.30.

It is strange.
Technically, you should have another stack trace with EnvInject plugin 0.33.

I just upgraded from 1.502 to 1.517 and 3/4 of my jobs disappeared from dashboard.
Projects are still on hdd, config files are there just 1.517 seems doesn't like them anymore.
Downgrading from 1.517 to 1.502 is working and all jobs are back, was there a config.xml format change as I can't find a word about it in the changelog.

Following error poped up into log (for each of the missing projects):
SEVERE: Failed Loading job 02-TEST_env
java.lang.NullPointerException
at hudson.plugins.promoted_builds.JobPropertyImpl.getItem(JobPropertyImpl.java:220)
at hudson.plugins.promoted_builds.JobPropertyImpl.getItem(JobPropertyImpl.java:41)
at hudson.model.AbstractProject.onLoad(AbstractProject.java:296)
at hudson.model.Items.load(Items.java:221)
at hudson.model.ItemGroupMixIn.loadChildren(ItemGroupMixIn.java:99)
at hudson.plugins.promoted_builds.JobPropertyImpl.setOwner(JobPropertyImpl.java:145)
at hudson.plugins.promoted_builds.JobPropertyImpl.setOwner(JobPropertyImpl.java:41)
at hudson.model.Job.onLoad(Job.java:201)
at hudson.model.AbstractProject.onLoad(AbstractProject.java:287)
at hudson.model.Project.onLoad(Project.java:83)
at hudson.model.Items.load(Items.java:221)
at jenkins.model.Jenkins$17.run(Jenkins.java:2542)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:146)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:259)
at jenkins.model.Jenkins$7.runTask(Jenkins.java:893)
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:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:679)
05-Jun-2013 12:31:44 jenkins.InitReactorRunner$1 onTaskFailed

Just ran into this - Some plugins were uninstalled when I upgraded, when I re-installed the plugins, my jobs showed up. Check to make sure your jobs still exist in the jobs directory on your master node.

I'd report the bug as plugins are being uninstalled when upgrading.

Not a core issue (but core got more robust against buggy plugins in 1.545 and 1.558, so that might be worth a try!)

New version of EnvInject API plugin cleaned up all such issues.

FSTrigger plugin needs to update to this new EnvInject API Plugin instead of EnvInject lib.