When I delete a clipping in the middle of my Clippings file, it automatically jumps to the end of the file. I have Logos 4.2a (4.21.5.0550 Beta) on Windows Vista.
more info - it works fine if you are at the top (beginning) of the Clippings file, as in it doesn't jump to the bottom. But if you delete a note from the middle of the file, it will jump to the bottom of the whole Clippings file.