This question already has an answer here:
I just refactored my project's entire codebase. So much so that even though it uses most of the same code base, things work in a radically different way. If the old version was 1.0, the new one would be 2.0. The project itself is just under 1mb in size (its a tiny little lib). I started the project a long time ago and its undergone many changes... so many that my git folder is now over 3mb in size.
In this case 3mb is a very small amount of data, but from a 'big picture' perspective, when should you cut your previous VCS history out of your current project and start over? Or should you never ever do this?