Each time you upload, a new "Version #" is assigned (internally) to the model.
The external model# does not change, and the file name is whatever you uploaded.
The older versions of the model are kept.
Part of the reason for this is so that if you upload a model and order it, then change the model before it gets printed, you will get what you paid for: the first version (no changes allowed during the order stream).
If you upload any new version of a model, even if it is the same exact file as the previous time, that Version# is increased, and is then treated as though it has not been printed before. This is by design.. their system can't be sure whether you changed the model or not.
I
have received in the past emails from Production "this model is particularly troublesome", but I will cut Shapeways some slack.. developing a method for that to be done on a consistent basis by 3rd party production teams (that may not speak my native language) is difficult. I don't know the specifics of how the files are transferred to the 3rd party. Imagine if they were sent over by CD.. there's no place to send messages (back)
Patience, Persistance, Politeness - the 3Ps will help us get us to Perfect Printed Products <grin>