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If you are able to confirm that it is actually some aspect of the content of the build.xml files that triggers the problem, that would give me a place to start. But I doubt that is the case.
XStream is indeed complex, though it is not clear that this is actually the source of the problem anyway. That hypothesis would be strengthened if a debugger shows that Run.reload is calling unmarshal(this) on the correct build.xml with correct <checkouts> yet after the call the checkouts field remains null.
My current hypothesis is that two copies of the same WorkflowRun are getting loaded, one with all fields restored, one without, and that the webhook request is getting routed to the bad one. You can create a custom logger on hudson.model.Run recording messages at FINER, looking for the reload message to see if the same build (myproject #123) is being loaded twice (@abc123 vs. @def456).