I set up several layers (base of footing, base of slab, floor level etc). I started drawing a wall on the 4th level prior to do anything else. When I clicked "Save and Update" all the levels disappeared.
I tried using this tool when it first came out and there seemed to be a bug and Andrew asked somebody to look at it. Generally it seemed to work fine if I always started drawing from the lowest level and worked my way up. The problems seemed to appear when I started inserting layers. I'm not sure if it's in any way related to that issue.