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Actually JENKINS-23130 is likely a symptom to this problem.
We use GerritTrigger a lot, I'm wondering if it has something to do with this.
Anyway, we just watched this happen in the wild...
We had build 482 at 3:04pm.
We then kicked off builds 483, 484, 485 at 4:09am, 4:12am, and 4:28 all submitted by Gerrit Trigger.
483, 484, and 485 weren't showing up in the Jenkins Web UI but they were well formed on disk.
We then did a "Query and Trigger Gerrit Patches" and a new 483 was kicked off (stealing the build number from the previous 483).
Some how the RunMap lost track of the previous 483, 484, and 485.
And something between 485 and "Query and Trigger Gerrit Patches" caused nextBuildNumber to be lost (going back to 483 matching the Jenkins UI only showing up to build 482).