In assigning initial conditions (Run | Settings | Initial Conditions), the user is given the option of selecting an age range for each record by selecting the Ages checkbox. The default age range is the same as the age range that spans the class as defined in the Deterministic Transitions. For each cell beggining in the class, VDDT then assigns an age randomly from a uniform distribution spanning the age range defined in the Initial Conditions screen. It is very likeley that the way that ages are initialized will influence the final conditions, particularly if run times are short.
Your idea of using final age conditions to initialize ages for a new run makes sense. One question that you will need to resolve is: how long is it appropriate to run your VDDT models before extracting the age distribution? If your models represent current conditions which have only been present for 100 years, you may want to start with reference conditions then run your current conditions model from this starting point for 100 years to get the age distribution for your current conditions.