O rsync pode excluir arquivos no destino usando a sintaxe --delete. Se você deseja que ele substitua um arquivo inteiro por sua implementação de sincronização parcial, tente --whole-file.
Trechos do link :
-W, --whole-file With this option rsync's delta-transfer algorithm is not used and the whole file is sent as-is instead. The transfer may be faster if this option is used when the bandwidth between the source and destination machines is higher than the bandwidth to disk (especially when the "disk" is actually a networked filesystem). This is the default when both the source and destination are specified as local paths, but only if no batch-writing option is in effect.
--delete This tells rsync to delete extraneous files from the receiving side (ones that aren't on the sending side), but only for the directories that are being synchronized. You must have asked rsync to send the whole directory (e.g. "dir" or "dir/") without using a wildcard for the directory's contents (e.g. "dir/*") since the wildcard is expanded by the shell and rsync thus gets a request to transfer individual files, not the files' parent directory. Files that are excluded from the transfer are also excluded from being deleted unless you use the --delete-excluded option or mark the rules as only matching on the sending side (see the include/exclude modifiers in the FILTER RULES section).