Rclone dedup between 2 different paths

  1. rclone check src: dst: can output a list of files.
  2. feed that list to rclone delete src: --files-from

or maybe

  1. rclone dedupe src: dst: --dedupe-mode list
  2. feed that list to rclone delete src: --files-from

or maybe

  1. rclone mount src: /path/to/mount/src/
  2. rclone mount dst: /path/to/mount/dst/
  3. point any dedupe tool to /path/to/mount/src/ /path/to/mount/dst/

or maybe
https://forum.rclone.org/t/big-syncs-with-millions-of-files/40182