This is the main issue that bugs me with ST3. Any changes to the file system do not show up in the sidebar without a quit and restart. Luckily this is a quick process, but you do lose all undo/redo history. Even "Refresh Folders" doesn't solve it.
I would really like to see an option to force a refresh of the file list, and maybe a preference for how often to query the file system.
I am using Build 3047 on Mac OS 10.8.4.