As far as I know, there isn’t a way to download your algo from the live servers. To the best of my knowledge, algos will maintain whatever state they were uploaded in, so any file changes you make during the game will be reset before the next game. Regardless of what’s in the files, what you would download should be the same as what was uploaded.
That being said, there’s a workaround you could use. This post shares details on how you can install Requests at run time then pull files from a database external to the servers, as well as how you can send data out. Using that, you could read/write changes and have your algo “evolve” over time. Do note however that network requests will probably be disabled at some point in the future, so this isn’t a sustainable option.
I’m not aware of any other workarounds for run-time changes/modifying behavior between matches.