I usually save my command history to version control every time I git commit. It helps a lot for less frequently visited projects.
You can set your HIST_FILE per project. That’s what I do in vscode (terminal env), so I have a history per project.
Other than that, I usually document some ops/quick read me about how to use or prepare the project
Yes, the lack of reproducibility is really Excel’s biggest weakness in data analysis. Is this 5th workbook that is a 4th generation derivation from the original data statistically valid? Can you go back to each step and verify it was valid? A script that does all processing and analysis starting from raw data can be validated and audited.