The problem was that App was running into an error. In order to prevent data overwriting, it checks to see if the subfolder (containing the results CSVs mentioned in my question) already exists, and raises an error if it does asking the user to move or rename the subfolder. The subfolder already existed when I called the app, and so it raised the error to stderr and I wasn't checking or catching that. I think the simplest fix is to have check = True in the subprocess call to confirm it is completing it properly.

This solution was mainly due to @axerotol who linked me to an answer where they were discussing subprocess calls in detail. This led me to assign the subprocess output to a variable which I then inspected in Spyder, which immediately highlighted the issue.