This is expected behaviour (deleting the chosen directory and creating it fresh), as it needs an empty directory to write the files into so that when it bundles it up, nothing extraneous is in there. I can add more warnings/tests/confirmation dialog boxes, though.

Okay, verified that this is actually happening, and it's because the wrong directory is being passed to vtkMRMLApplicationLogic::SaveSceneToSlicerDataBundleDirectory
it's getting passed the directory one level up from the one that's chosen.

Nicole's right - this should be in the Slicer4 bug tracker!

The problem seems to stem from the QFileDialog directory() call - it will return the currently displayed directory, so if you create a new directory and just click on it so that it appears in the Directory text box, directory() will still return the current directory one level up from the one that you created.
Will try to refactor the code to listen for the signal fileSelected instead.

svn 19471 uses getExistingDirectory() and confirms that the user wishes to proceed if there are files there.

Dear issue reporter,

Good news :) Slicer developers SOLVED the problem you reported - YOU now need to VERIFY and CLOSE this issue.