I came across this problem just now, because normally I would edit the parent page and then never touch it and only work on the sub/child pages.
So lets take the ArticlePage and ArticlePageHolder example from the tutorials which can be found here: Extending a Basic Site.
After editing the parent ArticlePageHolder and hitting the "Save & Publish" button, all child pages disappear and won't return until I refresh the tab on my browser with either 'F5' or Right Click > Refresh.
Now, my first thoughts was this could be a bug, but I also knew since it was something I hand coded to try and get a feel for creating these pages types, it could have been something I did that won't allow the tree to be updated after the save & publish function?
Any help would be awesome. I'm providing screenshots to show what happens and also providing my ArticlePage code and ArticlePageHolder code.
I was experiencing the same thing. It's like the jquery wasn't updating the tree properly when clicking Save and Publish. Refreshing the entire page fixed the problem, but it was a little disconcerting at first to see things disappear. I haven't seen the problem yet since upgrading to 3.0.2.