Jeweler's Toolkits are supposed to be able to remove them. If they aren't, then it's a bug. Or you might not be interacting with the window correctly?
Source: https://www.ddo.com/news/ddo-omg-dread-loot
Isle of Dread Augment Slots are unslotted just like any other Augment slot, so you can destroy a currently-slotted Augment by placing a new Augment into the slot or you can use a Jeweler's Toolkit to remove a slotted Augment
Edit: Apparently it is not a bug and it is DDO.com that is wrong, see Lynnabel's post below