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Thanks very much for the detailed investigation! I think that means this bug has the same symptoms as JENKINS-21980. Could you construct a Java based test case (in the git-plugin source code) which shows the failure? That would increase the chances of someone who knows the plugin finding a solution for the problem.
I think the issue is in the git-plugin handling of the case where a SHA1 was valid for a previous build, but is no longer valid. In that case, I assume the plugin should ignore the bad SHA1 and checkout something else instead. Do you have a recommendation for what should be used instead of the invalid SHA1?