I guess when you write "document" you mean "CAD Document". Isn't it?
Any way... I am quite sure there is a command utility to create via batch WTPart from existing CAD Document. It is used (as option) in the Pro/Intralink migration process. I think you can check in your environment and PTC guide/help. I am not sure if it gives you versions "allignement".
In windchill 10.x there is a preference to control version synchronization. I do not remember in 9.1
regards,
Vittorio