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If I can't fix pre-grad leaderswapping i'll probably disable it outright during the story. Then I'll leave instructions on how to reenable it via Skytemple in the changelog, with a warning of what might happen if you use it.
I sure know my version's going to keep leaderswapping and knowing me i'll forget to take it out of a future release, so it's probably the best option if I can't manage a true fix.