Comments on nodes clear when done in a specific way, it’s consistent within a new project as well. I’ve even rebuilt engine to double check.
For replicating the issue:
- Add a bubble comment to any node.
- Type in your comment, but instead of hitting enter to finalize comment click off somewhere in space.
- File > Refresh all nodes. It should reset your bubble text to either what it was before, or display “click to edit”
The issue does not occur when hitting enter, only when clicking off. I discovered it while preparing a toolkit for the marketplace. It’s unfortunate because many things trigger node refresh. I first noticed it when double clicking a custom event call to go to the event in my graph. It cleared the comment bubbles on several things so I decided to get to the bottom of it. 
I’ve attached two gifs, showing both ways if you’re curious and don’t want to open your engine for it.
This way works:
This way is rekt:
