All Items Get Deleted Upon Logout In Dungeoneering

If you log out while in a dungeon, any items you're wearing or have in your inventory get deleted.

This includes stuff you need and can't get back such as tools like the hammer, or other items needed to open certain skill doors. This also includes the gatestone.

Quick fix: Add all tools, hammer, knife, gatestone, etc to the shop npc. Make them have a 0 value to buy or to sell.