This is an expression that comes from the world of card games and is mostly used in American English. When you shuffle a pack of cards, you mix them up; you don’t know where a particular card is. When a plan or an idea gets lost in the shuffle, it doesn’t get the attention that it deserves. The expression can be used with reference to people as well.
Examples: In refugee camps, orphans often get lost in the shuffle and are left without food for days.