MacOS – OSX: How to compare and merge two folders and their subfolders and differing files of the same origin

I'm among those unlucky few (I'm hoping there are more than one) that are stuck with truly utterly messy backups from multiple machines, in multiple folders.

I've now managed to figure out that I've got one folder with 18gb and 44000+ files and one folder with 17gb and 34000+ files. They are the same folder, but one is on backup2/ and the other is in backup3/. I've used MacPaw's Gemini to remove duplicates from folder1 – and sometimes used Gemini to remove duplicates from folder2. They could be described as being totally out of sync with eachother – they are from separate times and now with mismatching files – i.e., there are duplicates there, but not really enough to use Gemini easily.

I'd like to compare and merge them, but safely. Without losing folders. One might have a subfolder inside a subfolder with 35 files, the other with 12 files – yet the 12 files wouldn't be in the 35 files, so I'd have to be able to merge subfolders so that I don't lose any files. Also, there are, as you would expect, duplicates there too, files with the same name, but with differing file content. I'd have to make copies of those to compare them, remove lines (in case of a textfile) from txt1 and add them to txt2, etc.

What should I do, and which app should I use to visually be able to combine these folders and their subfolders and their contents, merging the files and only keeping the ones that are absolutely differently sized (maybe I've touched a few of the files, maybe not, it's a total shambles).

How should I proceed? I'm running diff on the folders, but that's really quite complicated work.

I realize this is quite the complex question.