According to the documents, tagging is what you need.
To use tagging, you can use //. Every path after the // separator is considered to be “tagged” and will be treated as an original where possible
For example, rmlint a // b will tag "a" path as duplicate and "b" as a original path
In order to never delete any tagged files, there is the -k (--keep-all-tagged) option.
Another option would be -m (--must-match-tagged), which only looks for duplicates where there is an original in a tagged path.
An easy example (taken from the docs) would be: You have a portable backup drive with some old backups on it. You have just backed up your home folder to a new backup drive. You want to reformat the old backup drive and use it for something else. But first you want to check that there is nothing on the old drive that you don’t have somewhere else. The old drive is mounted at /media/portable.
$ rmlint --keep-all-tagged --must-match-tagged /media/portable // ~
Hope it helps!