Merging folders on a Mac is kind of a pain. When you do it, Finder tries to overwrite any file with the same name with the newer version. That means it’s easy to accidentally erase a whole folder. How-To Geek shows off a better way to merge folders using Terminal.
If you want to merge folders properly use the ditto command in Terminal. For example:
ditto ~/Desktop/Test ~/Downloads/Test
This will merge the Downloads/Test folder with the Desktop/Test folder, overwriting the contents of the destination folder with files from the source folder, while still keeping anything that’s different. You can also do this by option-clicking a folder and dragging and dropping it, but it doesn’t work as well. If you’ve been annoyed by Finder’s inconsistent merge options, ditto should do the trick.
How to Merge Folders on OS X Without Losing All Your Files (Seriously) | How-To Geek
via Lifehacker
Use the Ditto Command to Properly Merge Folders on Mac