fdupes - Compare files with checksum relative to each others path?

I've merged multiple backups together of all my photography files and came across multiple copies of many files. Not all files are copies and some are photoshopped ones. Now I noticed 'fdupes' that can help me identify duplicates and delete each.

Now there is one issue..

Let's say I've got this folder structure:

/Photoshoot X copy 1/*
/Photoshoot X copy 1/selection/*

/Photoshoot X copy 2/*
/Photoshoot X copy 2/selection/*

Many, if not all, files in copy 2 are duplicates of those in copy 1. Those can be deleted. However! Some, if not all, files inside the folder selection are direct duplicates of those found in the root folder. Those should not be deleted, even though they are duplicates. They should not be deleted because, even though they are duplicates, they are copied because these are the important ones out of the whole collection.

Now my question: is it possible to batch compare files relative to it's path?

So only both root folders are compared, not the root folder compared to the content of the folder selection.