diskDedupe will deduplicate files by replacing duplicate files with clones. The cloned files will keep all meta data of the replaced file, so modification time, creation time, links, aliases etc. will remain unchanged after deduplication.
Since clones use almost no space on the harddisk, the space of the duplicate file is reclaimed.
diskDedupe needs a filesystem that supports cloning of files. APFS on the Apple Platform is currently the only file system that supports this feature. If you select a volume or directory that does not support cloning (e.g. Mac OS Extended), diskDedupe will not be able to clone files and therefore cannot reclaim any diskspace.
Apple's macOS creates those warning messages for files that were changed by an application downloaded from the Mac App Store. We applied for an exemption and have provided an app version for which the operating system does not create those error messages, but that version did not get approved by Apple.
We continue to work with Apple’s Developer Support and App Review Team to address this issue. In the mean time, you can use this short how-to to remove the warnings set by Apple for files deduplicated with diskDedupe:
xattr -rl . | grep ";diskDedupe" | sed -e 's/:.*$//' | while read -r name; do xattr -d com.apple.quarantine "$name"; done
You can modify any file after deduplication. Unlike hard links, cloned files can be modified separately.