How to restore, I don't know. This bug reminds me of the mapgen bug Redcrab and some other servers had in the past with older minetest versions.
What version of minetest do you use, 0.4.10, 0.4.10-dev (or from where did you download minetest)? The latest development versions most of the time are running well.
In case you need to start a new. not corrupted world, but really want to take some old buildings with you, you might find world-edit usefull. It can copy/paste those buildings:
viewtopic.php?id=572#p4045