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The migration isn't technically necessary, since the folders were unpredictable before anyway and recreating the mount points can be done manually. (If these folders contain any user mountpoints then that means that the users knows how to do that)
It's just a "nice to have" so the upgrade shouldn't fail just because this failed.
P.S. sorry for the many PRs. Testing all aspects of this is very difficult. I hope this is the last one of them.