Locking the Version of a Document Used in a Flat Set
Next to each document in the set contents window there is a check box called Lock to Version. When off, the active version of the document will always be included in the set. When on, the set locks to the sequence number of the document's active version. This way, as new versions of the document are created and the active version's sequence number slides forward, the set will always use a fixed version of the document (specifically, the version which now has the sequence number that the active version had when the document was originally added to the set).
To use this feature, simply drag a document into a flat set and turn the check box on or off as needed.