What is the Purpose of the Wireframe and the Prototype?
These are specific tools used to communicate with some key differences:
- The wireframe communicates a layout and information/content heirarchy
- The prototype communicates to user flow and transition between pages
Assuming that you are getting feedback (from users and stakeholders) on the design as you go along, the latest design artifact should reflect the current feedback and best direction. Likely the prototype is the latest tool an is being refined to reflect the most current direction. This is normal.
As for the wireframe; has it already been shared and received feedback? Will a user, executive, or dev team see this artifact again? If not, then it has done its job and does not need to reflect the current design. If yes, it will get seen again then it should be changed to reflect the current design direction, but it also begs the question of why are you now using a wireframe and prototype for documenting the design?
Outside of coursework, you will find that one big problem in organizations is disparate models used to reflect and document a process. It is in part your responsibility to condense these disparate documents where you can; if the wireframe is no longer relevant, trash it. It has done its job and its time to move on to a current reflection of the design.