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Filenames are treated a bit differently on APFS. Not sure what else, but it seems there's a lot of other bizarre file metadata on OS X that you might want to sync.

edit: not really sure though, because it doesn't seem like this program cares about any of those metadata.

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It cares about those metadata a lot. Backups wont be bootable without it. And there is also disastrous data loss without it, a lot of files have their actual file data embedded in the metadata (resource forks et al). It's nuts because it's based on a 30 year old filesystem. That's one of the reasons why the smooth transition is impressive.

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