At first glance Collections and Folders in FontBase may seem like the same thing, but this is not really the case.
Folders in FontBase are the representation of folders as you have them on your computer. If you add a folder that has subfolders inside of it into FontBase, this folder structure will be kept when you view the folder in the Sidebar on the left side of the app window. If you delete a folder in FontBase, this will also remove the actual folder in your Root folder.
Collections, however, are constructs exclusive to FontBase. Creating and deleting a collection will not cause any changes in your Root folder or font files. Deleting or moving a font out of the Root folder will cause it to not be shown in the Collections it was added to. However, once your return the font back into the Root folder, it will show up in the respective Collections once again.