I'm not sure if this exactly meets your needs but here goes:
Open both Folders
Press common+A to select all the files in your Source folder. (either one in your case)
Drag the files and drop them into your Destination folder. (the other one in your case)
If any of the files you're copying over has the same name as a file in your destination folder, then a pop-up window will appear. It'll ask you to select one of the following:
Keep Both - This keeps both copies and renames the file you're copying to have "Copy."
Stop - This button cancels the copy altogether.
Replace - Pressing this replaces the file in the destination folder with the file from the source folder.
Skip - macOS hides this button, but if you hold down Option, the Keep Both button changes to Skip and will continue your transfer skipping the file in question.
The downside in your particular case is that you have to choose which Folder to act as Source and which as Destination. If you know for a fact that one of them is complete, that should be your Source as it copies over any files that are NOT in the Destination.
I suppose you could do this twice??? Choose one Folder as Source, copy over anything NOT in Source. Then repeat the procedure making the previous Source, the destination. I think that would work.
Ian