It's pretty difficult to answer this question without much detail. If I understand your question correctly, what will happen to the _current_ if the secondary connection is swapped?
I presume the connections on the secondary is polarity sensitive. So if the connection is backwards, the polarity is also backwards. Because the polarity is backward, there will be reverse phase sequence.
I found this great video on
http://generalpac.com where they talk about transformer connections and the importance of polarity marks. Here is the link to the video:
http://generalpac.com/index.php?option=com_content&view=article&id=101&Itemid=596Hope this helps!