When the server restarted, this happened... Walls and floors of invisible and untouchable blocks generated. Note that when you try to enter the block, you're "pushed" out of the area. The block has no physical appearance. Minecarts and mobs can enter the area. Blocks such as signs, redstone, and doors can be placed inside. You can enter via teleportation, for example, right clicking a minecart inside of the affected area.
We've tried WorldEdit, server restarting, and other things to fix it, and nothing has worked.