what you want is for Joplin to intelligently merge similar notes and that's not a simple job.
I use a tool called beyond compare that will bring up two versions of a document side by side and you can copy or move parts around. There are a number of tools like that but at the moment it's not part of Joplin.
On the desktop app, the notes in a duplicated folder can be ordered by update date and you can decide which one is later and then just remove the older one.
FWIW, I've allowed my Joplin cloud and Dropbox copies to diverge for months and I have over 300 diverged notes. At least I can go through and see if any of them are inane drivel now.