Normally, when uploading code, you program the firmware/software of the atmega256rfr2 chip (the big one). However, there's also a atmega16u2 chip on the board (the smaller one), which handles USB -> serial conversion. Normally, you do not modify its firmware, it just does its thing.
If you replace the 16u2 firmware using "DFU" mode (which I think the scouts support), I think there is a chance that you replace it with a non-working firmware, which also stops doing DFU, preventing you from uploading another firmware to the 16u2. I'm not entirely sure how DFU mode is implemented, it might be safer than I think (e.g. just like uploading a normal sketch to the scout shouldn't be able to brick things, since you never replace the "bootloader" - a piece of code that takes care of uploading new sketches, which cannot overwrite itself).
Does that help?