If we are talking about your own iOS application, you can do whatever you want. A “structure” is just a module, like any other module; it is included in the application and is simply part of the application code, so if you rework it, the next update will receive a revision and new code that uses it, and there is no problem.
In OS X, however, it is possible to install the framework in a library where the application sees it. Obviously, in this case, code that uses structure must be careful about version control. Similarly, even on iOS, if you use your infrastructure as a way to transfer the module to other developers, you should try not to casually interrupt your existing code that uses your infrastructure.