We will be wiping the nether for 1.6 due to the additions of chests in fortresses and other goodies that did not exist prior to 1.6
That being said, I will have the old nether up for ONE TO TWO WEEKS so people can move their items and whatnot out of the nether before I take it down and replace it with a new nether.
So yeah. Get yo shiz out of the nether.