netbeans should have an option to close file tabs that no longer exist or to mark them red (or some other way) in the tab but still leave the tab open.  It's fine to have no contents for the file that was removed as long as the tab is identified and kept open.  Closing tabs is annoying because i often switch branches during development and every time i switch to a branch that doesn't have the file i'm working on, netbeans closes the tab and i have to re-open all of them when i switch back to the branch