k0d3g3ar
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k0d3g3ar's post in Weird permissions issue was marked as the answerI wanted to follow up on this, because I solved it. The issue was that the Unraid server exhibiting the problems was an upgraded server from a long time back (probably v5 or so) and the disks in there were formatted with ReiserFS (now deprecated). Well 75% of them were - two were XFS and 6 were ReiserFS. On one of the disks when I ran diagnostics on it, it came back with a small file integrity issue during the ReiserFS check run, and was fixable. When I then ran the auto fix on it, it corrected it and then all of a sudden I could rsync to the server without any file permission errors anymore. Of course that has meant that about 15TB of content is being replaced now from our production server, but that's ok - at least we have the backup running correctly now.
Thank you for anyone who has helped (in particular @JorgeB) who helped me get to the point where I could identify the issue and fix it.