I guess you are referring to "The OS configures the setting in a too
late stage during the boot process, only after the NTFS volume was
already mounted.", however the volume in question was mounted after
booting via Nautilus.

In any case I think rdiff-backup should handle this more gracefully,
since it is supposed to store backups even on filesystems that do not
support all filenames that the source filesystem supports.

-- 
rdiff-backup fails on file with unknown unicode character
https://bugs.launchpad.net/bugs/223280
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