Before WoD came out, the website had a difficult time matching our characters due to the combined servers of Mok'nathal and Silvermoon. However, an update has come out and everything is working correctly now.
However, if you claimed your characters before this update, it could have messed up and deleted those characters. Everyone should check the guild roster to make sure you have claimed all of your characters again.
This update allows you to update your character straight from the armory to our website.