https://bugzilla.samba.org/show_bug.cgi?id=13061

--- Comment #5 from Kevin Korb <rs...@sanitarium.net> ---
OK, now I understand what is going on.  It is a 2-part problem...
Rsync sees the source file as new because it does not exist in the target but
it fails to copy the file because the name conflicts with an existing file. 
That should abort the deletions (not sure why it isn't) but in the end rsync
sees the existing file as superfluous because there is no matching filename on
the source.

The --fuzzy option might fix this.  Using --delete-before instead of
--delete-after would delete then replace the file.

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