For anyone running into this, I figured out what the problem was. The android filesystem on the device seems blind to changes that have been made outside of android apps, so any changes to file structure made with the Chrome OS file app does not appear in android apps until device restart. To fix this, I started using an Android file app to copy the files.
Semi-related rant: if you are considering using Chrome OS to do "productivity" tasks, I would reconsider it. Android app integration is full of bugs and it's a nightmare to get anything done beyond browsing the web or consuming content. Additionally, android apps are evicted from memory all the time even with 8GB ram (which I paid more for specifically to avoid this problem), - anything you are working on is frequently lost when multi tasking (alt-tabbing). I should have bought a windows laptop instead.