When it merges a folder you don't lose anything that's already in a folder.

If there are duplicate files in a folder it will warn you and ask you if you want to over-write them with the new file, save both (in which case it will give them different names, one the original name and one named original(2)), or not move the file(s).

Usually - almost always, except for meaningless files like "License" or "readme," a file with the same name and the same size is actually the same file so move all and over-write everything.

For this program there are often tons of files so just click the button in the lower left corner that says "do this for all files" if that happens. 95%+ of the time, if you're installing completely new (for you) content, there won't be any file duplications anyway.