@jwcph I am not an expert in anything to do with this kind of thing so there may be much better ways to do this but I tend to save a new version of the code (with something like 001, 002, 003 etc at the end) in the Arduino IDE each time I upload to the board so I know I haven't lost what I was doing
Once I'm done I zip everything but the last one
I don't think that there's any way to keep history in the Arduino IDE so this is the best option I've found