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I have made a little more progress on the issue and figured out why (superficially) the problem only re-appeared yesterday. The jobs runs that are missing their checkouts are all from yesterday. The aforementioned job which had failed 4 times, for example has 1 failed build from early February and the remaining failed builds were from yesterday. If I move the builds from yesterday out of the builds dir and restart Jenkins, the build from February is fine and checkouts. None of the builds from yesterday are good though. So I am now attaching build-1.xml as well. The only diff of significance seems to be an extra entry beneath flow-build/hudson.plugins.git.util.BuildData/buildsByBranchName and the related change to flow-build/hudson.plugins.git.util.BuildData/lastBuild. I have tried to follow what is going on in the deserialization process of this file into a WorkflowRun object but I am afraid I am lost.