Are there any things in Linux that need to be started over from scratch?

I'm curious how software can be created and evolve over time. I'm afraid that at some point, we'll realize there are issues with the software we're using that can only be remedied by massive changes or a complete rewrite.

Are there any instances of this happening? Where something is designed with a flaw that doesn't get realized until much later, necessitating scrapping the whole thing and starting from scratch?