Used SD for Clone and....
 

Recently used SD to clone my master. Had a problem with the master and needed to go back to my original clone. When I used SD to put the clone back on the Master everything worked fine, but I ended with several symbolic link files that were not there before. I don't have them in front of me right now, but I believe they were Private, Etc, and Var. Where did those come from and why did were they created?

Did you use Disk Utility to restore?

Yes I did...was that the problem?

Yes: Disk Utility has a bug that shows these normally hidden folder. Their presence won't hurt anything, though.

There are various workarounds documented in Apple's support forum and/or knowledge base.