Greetings!
Enabling VSF on a 5406R chassis should not erase your configuration, or make any significant changes other than to update interface numbers to their VSF equivalents (e.g., A1, A2, A3 would become 1/A1, 1/A2, 1/A3, etc). That said, I would always recommend making a backup of your switch configuration prior to enabling VSF (or making any other major configuration changes, for that matter).
Be sure to review the VSF restrictions section of the Management and Configuration Guide (page 643) prior to enabling the feature on your switch.