I just tried this 3 times in a row after having to restart the program each time to refresh the My Websites/Projects window to make it reshow my files.
I highlighted a file I didn't need anymore to delete it, right click, chose delete, the file deletes just fine but then all the files disappear from the window (not refreshing the window) and they never reappear, waited 10 min while browsing the forums here to make sure it wasn't a lag thing.
Here are the things I tried which don't work to refresh it:
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F5
Tabbing off the Projects Window and retabbing on it (basically changed to the My Computer or Code Snippets tabs and then back again)
Changing to the Server tab and back
Closing the program completely and reopening it works, and closing the Website Project via the menu at the top works to make it reshow the locations.
Let me know if you need any other information on it