Im thinking there is a big chance the new visa will be declined due to breach of the current visa.
Of course, nothing is certain, and it's a situation bound to cause some concern, but from what we've seen on here in the past, INZ do sometimes pass small breaches of regulations if they come to light - there are lots worse things in the world than a few weeks' extra work, and they're actually trying to keep out those previously convicted of serious crime or potential terrorists. Just recently, someone told on a thread how a friend of his had just finally got a proper partnership visa, having been working in NZ on no visa for something like five years, with successive employers assuming he was a Kiwi. The INZ government does seem to act kindly towards genuine partnerships - they like to keep their Kiwis and Residents happy and in NZ, and if the price of doing that is allowing in their foreign significant et ceteras, they say okay.