If we go with this, every bot has to be updated with "on age 1 I need to dump all my chloroplasts"
Not necessarily. They can be dropped into the sim without chloroplasts and then make them.
after long long generations a robot can evolve not to rely on chloroplasts at all. What if we take that robot (DNA only) and put it into a new sim?
As I discovered in my sims a long time ago, that's a problem for any long-evolved bot. You take it out of a sim, drop into a new one and most likely it will not survive. That's because the bots that evolved alongside it are the proper environment for it, it adapted to them. It's not adapted to "being dropped into a new sim".
I have spent a long time designing a system where I evolve a robot that can kill any other robot in F1 mode
The whole point of the F1 mode is to keep conditions always the same, as they were originally designed. You do any changes to it and the bots will not work as before and ratings will change. So, if you want F1 mode, don't bother with ANY changes. If you want to improve the program and make it a more sophisticated model, then you should strive to make the sims as self-sufficient as possible. And that means "no repopulating". I never liked the sims with active repopulating, it always felt like a cludge, made to compensate for the fact that DB's ecosystems are often unstable. You implement this and you won't need that cludge.