That's no different than normal software engineering. We use version control software (VCS, like git) to deal with it. You can include your results in the track

That's no different than normal software engineering. We use version control software (VCS, like git) to deal with it. You can include your results in the tracked source. For what it's worth, using results from outdated source code is extremely suspicious. This is a frequent problem in software development where we have tests or benchmarks based on stale code, and it's almost always incorrect. I would not trust your results if they are not created with the most up to date version of your software at all.