Had 999 earth shards on my retainer. To test if he could hold multiple stacks I selected a stack of 600 earth shards from my inventory. I clicked to change the quantity to 1 and pressed enter to confirm, 1 shard was selected. I clicked entrust and poof, 600 earth shards went into oblivion.
This is disgustingly poor game design, for whatever reason they decided to not allow us to have more than 1 stack of shards, they should have made it block you from attempting to throw them all away like this. There is no warning message, it just accepts the instruction and the shard will dissapear.