I have a similar question/problem. I'm running ST3 3021 on OS X 10.8.3. The sidebar in ST3 does not update when I create or delete files from the terminal. (I don't recall having this problem until two or three weeks ago, and don't see it on Windows 7.)
If I could force-update the sidebar it would be a little less intrusive, but I haven't found a way to do that, so am forced to close and restart ST3 manually to get changes reflected in the sidebar.
Suggestions/education welcome. Is there another place I should file a report on this?