This is a game breaking bug that has been known since shortly after the game was released, see this thread: http://forum.bioware.com/topic/522745-in-hushed-whispers-lyrium-shard-bug/. I encountered this bug today, 6th December 2015, playing the game on PS4. I've looted 4/5 lyrium shards, but the last one is stuck up on a wall out of reach. My autosaves are both from after the group in this room was killed. My last manual save is from before I went to Redcliffe, and reloading means I will lose an entire evening of game play.
These days I don't have that much time to play computer games, so replaying an entire evening is not going to happen. I'm a big fan of Bioware games. but when a GAME BREAKING bug that's been known for more than a year is still not fixed, well, then I become extremely disappointed.
As it stands, unless someone can provide me with a workaround for this bug that does not involve reloading a savegame several hours of gameplay earlier, then my DA:I progress comes to a full stop here. If it does, this will also be the last Bioware game I buy, unless I get a full refund for this broken game.