Say you have files in /home/bridgenjoyer/Data, /mnt/Backup, and /mnt/data

So

for d in /home/bridgeenjoyer/Data /mnt/backup /mnt/data
 do
    find $d -type f -print0
  done | xargs -0 md5sum | sort

• generates a list of all plain files by path name
• runs md5sum on them, which outputs a checksum as “checksum filename”
• sorts them by checksum

So, for identical files, you get identical repeated checksum antries.

You can filter out repeated entries (e.g. using awk, a shell script, or python) and extract their name and path.

There are also various tools which deduplicate identical files by hard linking them, if they are on the same file system. These will get the same inode number shown with ls -l. You can find these tools in the Arch wiki.

Then you need a strategy how to organize these identical files. You cold put all files into an archive folder, tidy them up, and only make and keep backups which you don’t modify.