Well, as you can see from the picture bellow (taken from the Mini Breakout Board schematics on sheet 3), you can see that VBUS (the USB power input) and VIN are separated. So you shouldn’t have any issues with that. You should be able to have both the USB and the battery connected and unplug any of them without getting any issues on the board.
I did see that, but with just that my inexperience and lack of knowledge with electronics didn't make me sure enough to want to risk busting a third Edison. I tried it now thanks to your post though, and it worked, so thanks!