This bug is fixed by version 2.0.3 of the Unofficial Dawnguard Patch.It is not possible to loot the remains ('Soul Embers') of the Bonemen in the lair, even though the option to do so is presented when they die.Jumping up the bone pile until you almost touch the sparkling part of it will also summon the reaper. This same effect can be achieved using a Flames spell. Just move to the back of the room and cast a mine on the large pile of bones. This will summon his minions from below and draw him out for the fight. You can get around having to collect the Reaper gem fragments by scattering a few Fire Runes on the ground near him.Search his Ghastly Remains for your reward.' Failure to step out of the flying acid results in some nasty damage. The first part of combat must include dodging the disgusting vomit he sprays across the chamber. His glowing red eyes stare through you, and he’s immediately hostile, as are the Bonemen minions that also appear. The guide describes it as 'This ghostly stuff of nightmares is a hooded shadow armed with a massive axe. The Reaper carries a Daedra heart, thus implying it may be of Daedric origin.

If you are having trouble finding the gem fragments, they are always in a chest directly underneath one of the Ideal Masters (giant floating health-draining gems).The Prima Guide calls it 'Regional Activity: (Don’t Fear) The Reaper'. The Reaper 'quest' isn't actually a quest at all but just a unique encounter that requires special steps to trigger.

Skyrim soul fragments