where deduplication is the ability to compare duplicates and remove the duplicate (exact/unchanged) files.
Perhaps the tool/utility can be programmed to allow differential backups. In a nutshell one would checksum all new files and compare with the old files (after comparing permissions). Once you find one, delete the duplicated file then sym-link the new partial backup with the full backup.
on BSD unix:
ms snapshot oldsnapshot
find -d ../oldsnapshot | cpio -dpl -
rsync -aE source/ ./
where ../oldsnapshot is the old backup of your data
snapshot is the new backup
source is the thing you want to backup.