If you make changes to paper after initial conference submission, should you present updated version at conference?
I believe you should do what is better to the audience. 

In some disciplines/communities it is strongly assumed that conference participants read the abstracts/papers before the presentation, and expect the discussion to follow precisely the material that is published. In this case, of course, you could only comment briefly on the recent changes you've made.

In other fields (such as mine), the abstracts are used only as a means to (roughly) describe the topic of the presentation. It is quite normal to extend the actual talk beyond the scope of the abstract, or reduce the role of some pieces of research advertised in the abstract. In this case, I'd advise you to make a talk that is simply interesting for you and the audience. It can probably include both the original design and your contribution to its recent development. Make sure people in the room understand why  the changes were needed, how you have worked them out, and what is the benefits of your new architecture.