How can I merge two similar-but-not identical folders?
You can open Terminal and use one of the following (rsync would probably be the one for you if you want something that won't be completely lost if you halt the process):

The standard UNIX way

cp -R -v source/. destination


The geeky UNIX way (restartable)

rsync -vaEW source/ destination


The OSX "easy" way

ditto -V source destination


Source