I just lost 3000 DE in a raid as well as 1434 gold and 75234 elixir.
They didn't touch the drills but completely destroyed the storage. I had 51674 DE at the time of the raid and the storage is Level 5.
My understanding was that they could take 5% up to a maximum of 2000 DE. Something which has occurred to me numerous times as I place more emphasis on protecting my gold storages than my DE.
Has anyone else noticed this?
http://i.imgur.com/8hTdzH7l.jpg

