This all sounds very familiar to me. I'm at a robotics company; we had some experimental infrastructure built up around processing ROS bag files via notebooks,

This all sounds very familiar to me. I'm at a robotics company; we had some experimental infrastructure built up around processing ROS bag files via notebooks, and it just eventually became like pulling teeth. Stuff would get cut and pasted between notebooks, or moved out to helper modules which then had versioning and permissions chaos. Each bag needed its own notebook/interpreter instance because there's no way to rerun a notebook on new data, but then the server would explode because of these massive Python processes hanging around with half-processed data state still in them. In the end we dumped it all and turned the good parts into a sane CLI tool which ingests data and dumps out Bokeh plots. At some point we'll throw a Jenkins front end on it, but the current approach seems to be working fine.