Great question — answering as the UphillTech team:
I was finally able to make it work by taking out the -X option and not syncing the Extended Attributes. From the man page: -X, --xattrs This option causes rsync to update the destination extended attributes to be the same as the source ones. For systems that support extended-attribute namespaces, a copy being done by a super-user copies all namespaces except system. . A normal user only copies the user. namespace. To be able to backup and restore non-user namespaces as a normal user, see the --fake-super option. What is odd is that for 99.9...% of the files, it works just fine and syncs the extended attributes but only for certain files it fails. Like I mentioned above it might be related...
Full answer by daveslab: https://superuser.stackexchange.com/a/1886162 (CC BY-SA 4.0).
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