When you set up a sync folder with Selective Sync ON, the entire directory shows up with folders containing placeholder files. This is great because you can search these directories (with Alfred for example) and then just sync the file you want to use.
However, when you choose a folder and select "Remove from this device," the folder's contents and the folder itself turn into placeholders. Now you can no longer enter that folder and see what's inside, nor can you search it. This is really annoying. What I then tend to do is unsync the contents of each folder individually instead of unsyncing the folder.
It would really be great if, when you unsync a folder, it preserves the folders and only replaces the files with placeholders.