--compare-dest
é seu amigo aqui:
rsync -rvn --compare-dest /target/ /source/ /extra_target/
(Remova -v e -n depois de confirmar que funciona para você)
Aqui está uma sessão do shell mostrando:
dennis@lightning:~$ cd /tmp
dennis@lightning:/tmp$ mkdir rs1
dennis@lightning:/tmp$ touch rs1/f1
dennis@lightning:/tmp$ rsync -av rs1/ rs2/
sending incremental file list
created directory rs2
./
f1
sent 96 bytes received 34 bytes 260.00 bytes/sec
total size is 0 speedup is 0.00
dennis@lightning:/tmp$ touch rs1/f2
dennis@lightning:/tmp$ rsync -avn rs1/ rs2/
sending incremental file list
./
f2
sent 71 bytes received 18 bytes 178.00 bytes/sec
total size is 0 speedup is 0.00 (DRY RUN)
dennis@lightning:/tmp$ rsync -avn rs1/ rs3/
sending incremental file list
created directory rs3
./
f1
f2
sent 49 bytes received 15 bytes 128.00 bytes/sec
total size is 0 speedup is 0.00 (DRY RUN)
dennis@lightning:/tmp$ rsync -rnv --compare-dest /tmp/rs2/ rs1/ rs3/
sending incremental file list
created directory rs3
f2
sent 49 bytes received 15 bytes 128.00 bytes/sec
total size is 0 speedup is 0.00 (DRY RUN)