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Gregory, on the first upgrade, I have let the migration complete which took several hours. On the next restart, it started over again which prompted me to downgrade the plugin.
It seems the migration is triggered very early in Jenkins startup process. Maybe it can be triggered asynchronously after Jenkins has booted (and at least the web gui is made available). If a job hasn't been migrated yet, the build could trigger the migration. Aka lazy migration :-]