Is there a difference between an "update" to a scientific paper vs. a "new" paper in a scientific journal? I have been doing research with a professor of mine pertaining to the topic of a well-received paper he wrote several years ago. The original paper discussed a computer program that the professor wrote. The research I am doing consists of adding new features to the computer program and broadening the scope of what the program does. The work does not change the basic premise of the paper, but rather expounds upon it and adds new applied programming concepts that have broader implications for the field. The professor wishes to publish the results of our research as an "update" to his previous paper, using the same format and information as the original paper, but with new information discussing the features being added. 

Is this a common practice in academia? How are "updates" to scientific papers handled when submitting to journals? Will the paper be considered the same paper but only  republished with a new title and date or will it be considered a "brand new" paper of which I will have co-authorship?
Recently, I have had a very similar situation occur.  The original paper discussed and explained the theoretical and practical aspects of a scientific technique that we adapted; the second discussed and explained the programming automation of the technique.

My advisor and co-author advised me at the time that each paper has got to be unique, taking the lead from the previous one and adding new information, techniques etc.  The journal that I published in are quite happy to take on a follow up article, just as long as it is sufficiently unique.

So, in answer to your questions - it would most likely be a new paper for publication, make reference to the previous one, but place the emphasis on the new developments.