Upvote:1
Flash drives won't need to be removed from your luggage in most cases except in a hand search but your phone will. X-rays won't damage any properly built flash drives just as it doesn't cause damage to phones.
I advise against putting a flash drive, or any sensitive electronics, in checked-in luggage. The risk of it getting damaged is too high. And, airlines don't take responsibility for damaging such things when in checked-in luggage.