Jumping in here to say that I'm experiencing a very similar issue (a few months after this was posted) - was wondering if there was any resolution?
I did some initial Custom CSS changes, came back and did more a few days later. I clicked Publish Changes, everything seemed fine. When I reloaded, the Custom CSS field still had the old css in it, none of the new changes.
At some point, the changes did save, but now the changes aren't visible on the site where the chatbot is embedded. Some styles are showing...but not all, and unfortunately I have white text on a white convo bubble background 😬 cc @loud-crowd-60573