Use --compare-dest.
Da página do manual:
--compare-dest=DIR - This option instructs rsync to use DIR on the destination machine as an additional hierarchy to compare destination files against doing transfers (if the files are missing in the destination directory). If a file is found in DIR that is identical to the sender's file, the file will NOT be transferred to the destination directory. This is useful for creating a sparse backup of just files that have changed from an earlier backup.
primeiro verifique sua sintaxe com --dry-run
rsync -aHxv --progress --dry-run --compare-dest=folder2/ folder1/ folder3/
Então, quando você estiver satisfeito com a saída:
rsync -aHxv --progress --compare-dest=folder2/ folder1/ folder3/
Este link tem uma boa explicação do escopo --compare-dest.