In the Stargate Universe episode "Divided", it is said that the shuttle clamps have to be engaged in order for Destiny's shield to envelope the shuttle, protecting it during faster-than-light travel. If the shuttle was not protected by the shield, it would not enter into FTL with Destiny and would be vaporized.
In the same episode, it is also mentioned that there was an alien ship attached to Destiny. Why was this ship not destroyed when Destiny entered into FTL?
Alien ship detaching from Destiny (Source)