How to avoid duplicate files when setting up back-up system

I have several external back up disks that I want to consolidate to one larger external backup drive. The problem is about 95% of the files are on both external drives. Is there a software program or a way to not get duplicates to migrate to the new external disk?
When you are talking about 1000’s of files, individually deleting files is not feasible.

If duplicates files are present with same file names, you will get popup with “keep both”, “stop” and “Replace” message during the copy & paste process. So you can avoid duplicate files and then you can create backup of all overall received data files.

There is a way to avoid/remove files with a lot of programs. Long time ago I tried a lot of them, but I am mostly satisfied from DuplicateFilesDeleter, which I’d recommend!