Yes. It doesnt actually replace the folder, even though the computer says that, it actually merges them. But if you are really worried, then backup those folders (you can do another folder on your computer, name it something like "Original Stuff" and save them there in case you want to set everything as it was). Also remember what the Notes section said:
"The only thing that will be replaced is the character heads package, but don't worry it has every character in this edition and every XML2 mod released so far, also the main dangeroom icons are included in this pack so that every new mod and some npc have their own icons. "
Everything else is new, and wont replace anything.