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I'm having something similar; job disappears at some point after completion...some times even during the build.
This is Jenkins 1.554.1 on Java:
java version "1.6.0_30"
OpenJDK Runtime Environment (IcedTea6 1.13.3) (rhel-5.1.13.3.el5_10-x86_64)
OpenJDK 64-Bit Server VM (build 23.25-b01, mixed mode)
It impacts both jobs we use the Job DSL as well as for jobs that we don't use Job DSL to control.
We can "work around" the problem (without having to reload the whole config from disk, which has in the past caused problems with plugins like GerritTrigger) by doing one of the following:
1. Click 'configure' then immediately click 'save'. The jobs sometimes reappear. (In previous versions of Jenkins, but it isn't working in 1.554.1 apparently).
2. If we're lucky, we can click 'trends' and the build will be there. We click on it and the job magically reappears.
I've noticed that some jobs behave badly after updating plugins until I go in and click 'configure' and then 'save' immediately (without changing anything). I've looked at the config.xml and it does change, sometimes new elements get added, or plugin versions are bumped. I'm unsure if the config.xml changing is part of the problem/work-around or if saving just causes Jenkins to rescan things.
It's not reproducible, but if someone can suggest things they'd like us to record/look-at when it happens again I'd be happy to do it. I'm not a Java debugging expert, but I can pull some in.