Hi there,
The airline I work for has put at least 4 software mods onto the Bus FMGC's since I started.
It is the equipment that has to be certified not the whole a/c.
I have even carried out software updates on the line using a dataloader (either onboard or using a portable loader)
This applies to all a/c equipment and there are specific airworthiness notices which pertain to the various software which can be loaded. (AWN #43 is one)