I can think of a few.
Areas being damaged beyond reparation
Areas being tainted by the warp or other ... taint
Areas being declared holy (or heoric, for example this house belonged to the great BLA that did BLA)
Hubris (Yes I do really need 60000 square meters, I am after all the great BLA!)
Population growth followed by a great decline
Nid or Ork infection (hey if they can infect and live impossible to get rid of in a world why not a craft world)
Started production of one thing but found out they needed another so they left it half done
While none of these would explain a huge areas of terrain. It all adds up. After all Eldars are people too =)