Nope, the new layout wasn't due to the back-up. I was just anxious to try a portal layout and the newest version of YAPP portal system (based on the YaBB boards I use) was just released.
In fact, losing all of the messages had nothing to do with the portal layout at all. What had happened was I was tinkering around in the admin center and accidently clicked on "Delete all posts older than 30 days" !!
If you're anxious for reasons why I upgraded, visit the New Portal set up thread here