Checking the "Master" check box marks a folder as containing documents which are not to be replaced. The documents within a Master folder will replace the corresponding document in the other folder, EVEN IF THE OTHER DOCUMENT IS NEWER.
This feature is most useful in making an exact copy of an existing folder, when the contents of the other folder are in doubt. An example of such a situation is a folder on a file server which may have been changed, but which should contain a particular master set of documents.