Hi @farmer_giles. You might consider using the Git version control software:
In this way, you can store the entire revision history inside the sketch project itself instead of creating a copy of the project at each revision. You can add a description of each revision and easily switch to any point in the revision history.
Git is fairly complex, so I think the "caveman version control" system of creating a zillion copies of each project is appropriate for those who are just getting started with programming. But for those who are a bit more experienced I think it is well worth the effort to learn how to use Git.
If you find working from the command line to be inconvenient or intimidating, you should check out the various free "Git clients", which allow using Git from a user friendly GUI application instead of the command line:
https://git-scm.com/downloads/guis
There is a tutorial for using Git with Arduino projects here: