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I looked into the sources and it turned out that build graph is persisted in build.xml, but when it is loaded, it is overwritten by field initializer in FlowRun.java.
Also, in JobInvocation.groovy some build fields are returned without using getBuild() method, so lazy wiring JobInvocation object with actual Build object is skipped causing all builds displayed as not started on a graph loaded from disk.
Sending a pull request for this fix.