It has become clear that the Jupyter Notebook integration caches code and does not appropriately clear when there are changes made - resulting in "saved" workflows that do not contain updated code. This happens when two people are using a "shared" workflow (emailed back and forth or from a shared drive) if one person does not completely shut down out of Designer Desktop if they had previously had the workflow open at any point. This has been confirmed by Alteryx Support and is not just my hunch.
This also happens sometimes with a single user - where the Jupyter Notebook save button has been pressed multiple times and the workflow has been saved, but the changes do not make it to the file.
The integration is a step in the right direction for sure and is great to use - but my idea is that the cache should be attached to the workflows, not the entire session of Designer. Not knowing if changes were actually saved, and discovering that some were not is extremely frustrating.