What you are experiencing is a problem with the connection between your game and the server which is bad enough to stop your game from properly retrieving your game progress from the server but not bad enough that your connection gets terminated.
GW2 saves all your game progress on the servers and not on your machine and the game constantly references the server to figure out what to show you and what you have; temporary communication problems which prevent the game from retrieving the information hit every once in a while and when that happens the game doesn't know what you have or don't have so you "lose" everything.
When this happens just turn off the game and do something else for awhile and the next time you log on you should find all your stuff back again just fine. It's happened two or three times to me over the last year and it's always temporary.